Variant report

Variant	rs72691012
Chromosome Location	chr1:146711400-146711401
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr1:146710349-146711468	HepG2	liver:	n/a	n/a
2	NFIC	chr1:146709175-146712072	HepG2	liver:	n/a	n/a
3	HEY1	chr1:146710395-146711463	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:146710539-146711551	HepG2	liver:	n/a	n/a
5	FOXA2	chr1:146709314-146711469	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:146710601-146712132	HepG2	liver:	n/a	n/a
7	ARID3A	chr1:146709548-146711502	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:146710385-146712438	HepG2	liver:	n/a	n/a
9	MYBL2	chr1:146709441-146711507	HepG2	liver:	n/a	n/a
10	HEY1	chr1:146710483-146712180	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:146669479..146672261-chr1:146708761..146711496,2	MCF-7	breast:
2	chr1:146655417..146657145-chr1:146709570..146711892,2	MCF-7	breast:
3	chr1:146642343..146646438-chr1:146707270..146711599,11	MCF-7	breast:
4	chr1:146614774..146616366-chr1:146710035..146712761,2	K562	blood:
5	chr1:146638044..146647556-chr1:146707628..146717159,48	MCF-7	breast:

No data

Variant related genes	Relation type
CHD1L	TF binding region
ENSG00000273071	Chromatin interaction
ENSG00000271721	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000131791	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11239954	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239958	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800580	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12046706	0.89[EUR][1000 genomes]
rs12060046	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17159914	0.89[EUR][1000 genomes]
rs17159924	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17160050	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17160051	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17355474	0.82[AMR][1000 genomes]
rs17355509	0.82[AMR][1000 genomes]
rs17356184	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17356219	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17356233	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17356240	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17356492	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17360443	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1932977	0.91[EUR][1000 genomes]
rs1999820	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2083720	0.82[AMR][1000 genomes]
rs2354428	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28381210	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2883323	0.87[EUR][1000 genomes]
rs2883324	0.87[EUR][1000 genomes]
rs2883434	0.88[EUR][1000 genomes]
rs3737855	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766519	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3766520	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3766522	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4301678	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4373796	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4453096	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4568882	0.87[EUR][1000 genomes]
rs4593887	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4950308	0.81[AMR][1000 genomes]
rs4950313	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4950315	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4950316	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4950318	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4950319	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4950371	0.81[AMR][1000 genomes]
rs4950379	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4950382	0.89[EUR][1000 genomes]
rs4950384	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4950389	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4950392	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4950409	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56080828	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6703892	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72691004	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72691016	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691025	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72691032	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72691033	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72691041	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72691054	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72691090	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72691093	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691095	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72691097	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72691098	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72691102	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692904	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692905	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692907	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692914	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692917	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72692942	0.87[EUR][1000 genomes]
rs72692963	0.87[EUR][1000 genomes]
rs72692965	0.87[EUR][1000 genomes]
rs72692968	0.87[EUR][1000 genomes]
rs72692971	0.87[EUR][1000 genomes]
rs72692973	0.87[EUR][1000 genomes]
rs72692975	0.87[EUR][1000 genomes]
rs72692979	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72692980	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72706441	0.82[AMR][1000 genomes]
rs72708536	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7514970	0.81[AMR][1000 genomes]
rs7554833	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
3	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
7	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
15	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv872257	chr1:146643555-146724923	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv437047	chr1:146643555-146841602	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
22	nsv1005809	chr1:146647822-146886419	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv535134	chr1:146647822-146886419	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
25	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
26	nsv547676	chr1:146686228-146996047	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
27	nsv872259	chr1:146688941-146724923	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs72691012	RP11-337C18.8	cis	Thyroid	GTEx
rs72691012	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146705800-146711600	Enhancers	Stomach Mucosa	stomach
2	chr1:146707600-146713000	Enhancers	Fetal Intestine Large	intestine
3	chr1:146708800-146712200	Enhancers	Fetal Intestine Small	intestine
4	chr1:146708800-146713600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:146709000-146713600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:146709200-146711800	Weak transcription	Lung	lung
7	chr1:146709200-146712000	Enhancers	Liver	Liver
8	chr1:146709200-146713600	Weak transcription	HMEC	breast
9	chr1:146709200-146713800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:146709200-146714200	Weak transcription	Gastric	stomach
11	chr1:146709400-146711600	Enhancers	Duodenum Mucosa	Duodenum
12	chr1:146709400-146713600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:146709400-146713800	Weak transcription	Colonic Mucosa	Colon
14	chr1:146709400-146713800	Weak transcription	Placenta	Placenta
15	chr1:146709400-146714000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:146709400-146714000	Weak transcription	Esophagus	oesophagus
17	chr1:146709400-146714200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:146710200-146711600	Enhancers	A549	lung
19	chr1:146710200-146712600	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr1:146710200-146713400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:146710200-146713600	Weak transcription	Hela-S3	cervix
22	chr1:146710200-146713800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:146710400-146711600	Enhancers	Fetal Lung	lung
24	chr1:146710600-146712600	Enhancers	Pancreas	Pancrea
25	chr1:146710800-146713200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:146711000-146711800	Flanking Active TSS	HepG2	liver
27	chr1:146711200-146711600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:146711200-146713000	Enhancers	Fetal Kidney	kidney
29	chr1:146711200-146713600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:146711200-146713800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr1:146711400-146711600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:146711400-146712600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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