Variant report

Variant	rs2354431
Chromosome Location	chr1:146697471-146697472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr1:146696352-146697472	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:146696690-146697597	GM12878	blood:	n/a	n/a
3	ELF1	chr1:146696574-146697561	MCF-7	breast:	n/a	chr1:146697215-146697228

No.	Distal block	Cell Line	Cell type
1	chr1:146642336..146645437-chr1:146695438..146700629,5	MCF-7	breast:
2	chr1:146554322..146556284-chr1:146695615..146697996,2	K562	blood:
3	chr1:146696837..146698411-chr1:146712690..146714325,2	K562	blood:
4	chr1:146642791..146647744-chr1:146694916..146698486,10	MCF-7	breast:
5	chr1:146554322..146557448-chr1:146695605..146698369,3	K562	blood:

Variant related genes	Relation type
FMO5	TF binding region
ENSG00000237188	Chromatin interaction
ENSG00000230832	Chromatin interaction
ENSG00000271721	Chromatin interaction
ENSG00000273071	Chromatin interaction
ENSG00000131791	Chromatin interaction
ENSG00000131778	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10793652	0.95[ASN][1000 genomes]
rs10793653	0.95[ASN][1000 genomes]
rs10900326	0.98[ASN][1000 genomes]
rs10900327	0.96[ASN][1000 genomes]
rs11239950	0.95[ASN][1000 genomes]
rs11239951	0.95[ASN][1000 genomes]
rs12139680	0.95[ASN][1000 genomes]
rs12144240	0.83[ASN][1000 genomes]
rs2289575	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6657920	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6658030	0.98[ASN][1000 genomes]
rs6668690	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6675377	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71510593	0.95[ASN][1000 genomes]
rs71510594	0.81[ASN][1000 genomes]
rs7517655	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	nsv872258	chr1:146662018-146709784	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
28	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
29	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2354431	CHD1L	cis	Whole Blood	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146695400-146697800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:146695400-146697800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:146695400-146698000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:146695600-146697800	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:146696200-146697600	Active TSS	Colonic Mucosa	Colon
6	chr1:146696400-146697600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:146696400-146697600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:146696400-146697600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:146696400-146697600	Active TSS	Fetal Intestine Large	intestine
10	chr1:146696400-146697600	Active TSS	Placenta	Placenta
11	chr1:146696400-146697600	Active TSS	Ovary	ovary
12	chr1:146696400-146697600	Active TSS	Right Atrium	heart
13	chr1:146696400-146697600	Active TSS	NH-A	brain
14	chr1:146696400-146697800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:146696400-146697800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:146696400-146697800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:146696400-146697800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:146696400-146697800	Active TSS	Fetal Intestine Small	intestine
19	chr1:146696400-146697800	Active TSS	Fetal Kidney	kidney
20	chr1:146696400-146697800	Active TSS	Thymus	Thymus
21	chr1:146696400-146697800	Active TSS	Osteobl	bone
22	chr1:146696400-146698000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:146696400-146698000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:146696400-146698000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:146696400-146698000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:146696600-146697600	Active TSS	H1 Cell Line	embryonic stem cell
27	chr1:146696600-146697600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:146696600-146697600	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr1:146696600-146697600	Active TSS	Primary T cells from cord blood	blood
30	chr1:146696600-146697600	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:146696600-146697600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr1:146696600-146697600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:146696600-146697600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:146696600-146697600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:146696600-146697600	Active TSS	Aorta	Aorta
36	chr1:146696600-146697600	Active TSS	Brain Anterior Caudate	brain
37	chr1:146696600-146697600	Active TSS	Brain Hippocampus Middle	brain
38	chr1:146696600-146697600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:146696600-146697600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr1:146696600-146697600	Active TSS	Right Ventricle	heart
41	chr1:146696600-146697600	Active TSS	HUVEC	blood vessel
42	chr1:146696600-146697600	Active TSS	NHLF	lung
43	chr1:146696600-146697800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr1:146696600-146697800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:146696600-146697800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr1:146696600-146697800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:146696600-146697800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:146696600-146697800	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:146696600-146697800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:146696600-146697800	Active TSS	Fetal Muscle Trunk	muscle

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