Variant report

Variant	rs72997577
Chromosome Location	chr1:146710629-146710630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr1:146710584-146711219	HepG2	liver:	n/a	chr1:146710899-146710914
2	JUND	chr1:146710604-146710794	HepG2	liver:	n/a	n/a
3	RXRA	chr1:146710533-146711178	HepG2	liver:	n/a	n/a
4	TBP	chr1:146710608-146711226	HepG2	liver:	n/a	n/a
5	ZBTB7A	chr1:146710504-146710765	HepG2	liver:	n/a	n/a
6	HDAC2	chr1:146710515-146711252	HepG2	liver:	n/a	n/a
7	MBD4	chr1:146710349-146711468	HepG2	liver:	n/a	n/a
8	FOXA1	chr1:146710452-146711230	HepG2	liver:	n/a	n/a
9	RXRA	chr1:146710469-146711067	HepG2	liver:	n/a	n/a
10	TEAD4	chr1:146709624-146711177	HepG2	liver:	n/a	n/a
11	FOSL2	chr1:146710498-146711116	HepG2	liver:	n/a	n/a
12	NFIC	chr1:146709175-146712072	HepG2	liver:	n/a	n/a
13	TCF7L2	chr1:146710601-146710929	HepG2	liver:	n/a	n/a
14	HEY1	chr1:146710395-146711463	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:146710539-146711551	HepG2	liver:	n/a	n/a
16	EP300	chr1:146710437-146711226	HepG2	liver:	n/a	n/a
17	FOXA2	chr1:146709314-146711469	HepG2	liver:	n/a	n/a
18	FOXA1	chr1:146710485-146711222	HepG2	liver:	n/a	n/a
19	MYBL2	chr1:146710393-146711196	HepG2	liver:	n/a	n/a
20	FOXA2	chr1:146710482-146711146	HepG2	liver:	n/a	n/a
21	FOSL2	chr1:146710562-146711160	HepG2	liver:	n/a	n/a
22	FOXA1	chr1:146710416-146711300	HepG2	liver:	n/a	n/a
23	CEBPB	chr1:146710500-146710632	HepG2	liver:	n/a	n/a
24	TCF12	chr1:146710532-146711099	HepG2	liver:	n/a	n/a
25	NFIC	chr1:146710497-146711116	HepG2	liver:	n/a	n/a
26	FOXA1	chr1:146710413-146711273	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:146710601-146712132	HepG2	liver:	n/a	n/a
28	GATA2	chr1:146710453-146710836	K562	blood:	n/a	n/a
29	ARID3A	chr1:146709548-146711502	HepG2	liver:	n/a	n/a
30	HNF4G	chr1:146710525-146711225	HepG2	liver:	n/a	n/a
31	JUND	chr1:146710585-146711139	HepG2	liver:	n/a	n/a
32	HNF4G	chr1:146710605-146711273	HepG2	liver:	n/a	n/a
33	POLR2A	chr1:146710385-146712438	HepG2	liver:	n/a	n/a
34	EP300	chr1:146710362-146711257	HepG2	liver:	n/a	n/a
35	MYBL2	chr1:146709441-146711507	HepG2	liver:	n/a	n/a
36	SP1	chr1:146710433-146711243	HepG2	liver:	n/a	n/a
37	HEY1	chr1:146710483-146712180	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:146669479..146672261-chr1:146708761..146711496,2	MCF-7	breast:
2	chr1:146694787..146699847-chr1:146706639..146711306,10	MCF-7	breast:
3	chr1:146555582..146557565-chr1:146708158..146710932,2	K562	blood:
4	chr1:146655417..146657145-chr1:146709570..146711892,2	MCF-7	breast:
5	chr1:146636327..146637904-chr1:146709473..146711189,2	MCF-7	breast:
6	chr1:146642343..146646438-chr1:146707270..146711599,11	MCF-7	breast:
7	chr1:146614774..146616366-chr1:146710035..146712761,2	K562	blood:
8	chr1:146554799..146556804-chr1:146709237..146711189,2	K562	blood:
9	chr1:146581119..146583919-chr1:146708299..146710988,2	MCF-7	breast:
10	chr1:146638044..146647556-chr1:146707628..146717159,48	MCF-7	breast:

No data

Variant related genes	Relation type
CHD1L	TF binding region
ENSG00000131791	Chromatin interaction
ENSG00000131781	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000271721	Chromatin interaction
ENSG00000237188	Chromatin interaction
ENSG00000230832	Chromatin interaction
ENSG00000236806	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs28745890	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58276129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58820837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59402704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59689147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60063927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60107727	0.85[AFR][1000 genomes]
rs60565795	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6672821	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6702705	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995589	1.00[AMR][1000 genomes]
rs72995597	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997505	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997514	1.00[AMR][1000 genomes]
rs72997527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997590	0.87[AFR][1000 genomes]
rs72999623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999634	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999637	1.00[AMR][1000 genomes]
rs72999638	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999639	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72999640	1.00[AMR][1000 genomes]
rs72999646	1.00[AMR][1000 genomes]
rs72999648	1.00[AMR][1000 genomes]
rs72999655	1.00[AMR][1000 genomes]
rs72999656	1.00[AMR][1000 genomes]
rs7526114	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7527846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7535451	1.00[AMR][1000 genomes]
rs7536442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7546133	1.00[AFR][1000 genomes];1.00[AMR][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

No data

Chromatin state (count:29 , 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	chr1:146708400-146711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:146708800-146712200	Enhancers	Fetal Intestine Small	intestine
5	chr1:146708800-146713600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:146709000-146713600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:146709200-146711800	Weak transcription	Lung	lung
8	chr1:146709200-146712000	Enhancers	Liver	Liver
9	chr1:146709200-146713600	Weak transcription	HMEC	breast
10	chr1:146709200-146713800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:146709200-146714200	Weak transcription	Gastric	stomach
12	chr1:146709400-146710800	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr1:146709400-146711000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:146709400-146711600	Enhancers	Duodenum Mucosa	Duodenum
15	chr1:146709400-146713600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:146709400-146713800	Weak transcription	Colonic Mucosa	Colon
17	chr1:146709400-146713800	Weak transcription	Placenta	Placenta
18	chr1:146709400-146714000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:146709400-146714000	Weak transcription	Esophagus	oesophagus
20	chr1:146709400-146714200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:146710200-146711600	Enhancers	A549	lung
22	chr1:146710200-146712600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr1:146710200-146713400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:146710200-146713600	Weak transcription	Hela-S3	cervix
25	chr1:146710200-146713800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:146710400-146711600	Enhancers	Fetal Lung	lung
27	chr1:146710600-146711000	Enhancers	HepG2	liver
28	chr1:146710600-146711200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:146710600-146712600	Enhancers	Pancreas	Pancrea

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