Variant report

Variant	rs3752026
Chromosome Location	chr17:38804561-38804562
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:265)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:265 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38803330-38804728	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr17:38803276-38805169	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr17:38803632-38804897	HCT-116	colon:	n/a	n/a
4	MAX	chr17:38803829-38804719	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr17:38804470-38804806	Hela-S3	cervix:	n/a	n/a
6	IRF1	chr17:38803930-38804680	K562	blood:	n/a	n/a
7	SIN3AK20	chr17:38804452-38804937	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr17:38803593-38804878	GM18951	blood:	n/a	n/a
9	YY1	chr17:38803723-38804918	HepG2	liver:	n/a	chr17:38804426-38804437
10	ELF1	chr17:38803786-38804712	K562	blood:	n/a	n/a
11	RUNX3	chr17:38803444-38804941	GM12878	blood:	n/a	n/a
12	MAX	chr17:38803723-38805066	ECC-1	luminal epithelium:	n/a	n/a
13	ELF1	chr17:38803514-38804762	GM12878	blood:	n/a	n/a
14	POLR2A	chr17:38803567-38805314	H1-neurons	neurons:	n/a	n/a
15	HEY1	chr17:38803568-38805200	K562	blood:	n/a	n/a
16	E2F6	chr17:38804294-38804984	K562	blood:	n/a	n/a
17	GTF2F1	chr17:38803527-38804804	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr17:38803542-38804806	K562	blood:	n/a	n/a
19	POLR2A	chr17:38804191-38804755	GM12891	blood:	n/a	n/a
20	POLR2A	chr17:38803764-38805055	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr17:38803099-38804908	GM12878	blood:	n/a	n/a
22	POLR2A	chr17:38804189-38804634	SK-N-SH	brain:	n/a	n/a
23	HEY1	chr17:38803708-38804977	K562	blood:	n/a	n/a
24	MYBL2	chr17:38803471-38805342	HepG2	liver:	n/a	n/a
25	MAX	chr17:38803617-38804755	HepG2	liver:	n/a	n/a
26	TAF1	chr17:38803645-38804915	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr17:38803512-38805012	MCF10A-Er-Src	breast:	n/a	n/a
28	CHD2	chr17:38803931-38804958	HepG2	liver:	n/a	chr17:38804392-38804402
29	ELF1	chr17:38803661-38804678	A549	lung:	n/a	n/a
30	POLR2A	chr17:38804154-38804851	GM12892	blood:	n/a	n/a
31	POLR2A	chr17:38803686-38804782	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr17:38804207-38804904	GM12878	blood:	n/a	n/a
33	POLR2A	chr17:38803572-38805013	HL-60	blood:	n/a	n/a
34	STAT5A	chr17:38803382-38804829	GM12878	blood:	n/a	n/a
35	TAF1	chr17:38803685-38805346	H1-neurons	neurons:	n/a	n/a
36	MYC	chr17:38803930-38804975	K562	blood:	n/a	n/a
37	HCFC1	chr17:38802737-38805126	Hela-S3	cervix:	n/a	n/a
38	MAX	chr17:38804255-38804908	H1-hESC	embryonic stem cell:	n/a	n/a
39	HNF4G	chr17:38804002-38804743	HepG2	liver:	n/a	chr17:38804567-38804582 chr17:38804485-38804493 chr17:38804567-38804582
40	MAZ	chr17:38803594-38804843	GM12878	blood:	n/a	n/a
41	HEY1	chr17:38803424-38805302	HepG2	liver:	n/a	n/a
42	SP4	chr17:38803896-38804729	H1-hESC	embryonic stem cell:	n/a	n/a
43	TAF1	chr17:38803853-38804759	GM12892	blood:	n/a	n/a
44	TCF7L2	chr17:38803693-38804651	HCT-116	colon:	n/a	n/a
45	ELF1	chr17:38803487-38804933	GM12878	blood:	n/a	n/a
46	MAX	chr17:38803628-38804886	NB4	blood:	n/a	n/a
47	TCF12	chr17:38803843-38804896	ECC-1	luminal epithelium:	n/a	n/a
48	TAF1	chr17:38803512-38804848	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr17:38804173-38804801	GM12891	blood:	n/a	n/a
50	RELA	chr17:38803548-38804804	GM15510	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38802991..38805061-chr17:38975232..38977331,2	K562	blood:
2	chr17:38802997..38805414-chr17:38859614..38861857,2	MCF-7	breast:
3	chr17:38791360..38793414-chr17:38804044..38805611,2	K562	blood:
4	chr17:38804020..38805586-chr17:38953834..38956607,2	MCF-7	breast:
5	chr17:38803836..38805956-chr17:38820835..38822602,2	MCF-7	breast:
6	chr12:123717306..123718025-chr17:38804001..38804932,2	Hela-S3	cervix:
7	chr17:38802728..38805352-chr17:39844385..39846294,2	MCF-7	breast:

No data

Variant related genes	Relation type
SMARCE1	TF binding region
ENSG00000173908	Chromatin interaction
ENSG00000073584	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000271876	Chromatin interaction
ENSG00000167920	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000167916	Chromatin interaction
ENSG00000130921	Chromatin interaction
ENSG00000213424	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1013971	0.81[ASN][1000 genomes]
rs1029792	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048572	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1048573	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11658582	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12943859	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2008469	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2014704	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2109223	0.84[EUR][1000 genomes]
rs2159430	0.82[EUR][1000 genomes]
rs2315020	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2429549	0.95[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs2462962	0.81[EUR][1000 genomes]
rs2462963	0.81[EUR][1000 genomes]
rs4890093	0.82[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4890117	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4890119	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6503547	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6503549	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7209467	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7209735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7210983	0.83[ASN][1000 genomes]
rs7219483	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7223332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7223354	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs726848	0.90[CEU][hapmap]
rs757411	0.89[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs8068721	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8076587	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917595	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9896791	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9900324	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9906785	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9915135	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS 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	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
5	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3752026	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs3752026	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs3752026	KRT24	cis	Esophagus Mucosa	GTEx
rs3752026	KRT32	cis	cerebellum	SCAN
rs3752026	CCL4	cis	parietal	SCAN
rs3752026	TBCA	trans	cerebellum	SCAN
rs3752026	TADA2A	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38802000-38805400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr17:38802400-38805000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr17:38802600-38804800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:38802600-38805000	Active TSS	K562	blood
5	chr17:38802600-38805000	Active TSS	NHLF	lung
6	chr17:38802600-38805400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr17:38802600-38805400	Active TSS	Psoas Muscle	Psoas
8	chr17:38802800-38804600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:38802800-38804600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:38802800-38805000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr17:38802800-38805200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr17:38802800-38805600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:38803000-38804800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:38803000-38805000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr17:38803000-38805000	Active TSS	Fetal Muscle Leg	muscle
16	chr17:38803000-38805000	Active TSS	Placenta	Placenta
17	chr17:38803000-38805000	Active TSS	Left Ventricle	heart
18	chr17:38803000-38805000	Active TSS	Pancreas	Pancrea
19	chr17:38803000-38805000	Active TSS	Placenta Amnion	Placenta Amnion
20	chr17:38803000-38805000	Active TSS	Right Atrium	heart
21	chr17:38803000-38805000	Active TSS	Small Intestine	intestine
22	chr17:38803000-38805000	Active TSS	HSMM	muscle
23	chr17:38803000-38805200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr17:38803000-38805200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr17:38803000-38805200	Active TSS	Ovary	ovary
26	chr17:38803000-38805200	Active TSS	Right Ventricle	heart
27	chr17:38803000-38805200	Active TSS	NHDF-Ad	bronchial
28	chr17:38803000-38805400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr17:38803000-38805400	Active TSS	Fetal Muscle Trunk	muscle
30	chr17:38803200-38804600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:38803200-38804800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:38803200-38804800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:38803200-38804800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr17:38803200-38804800	Active TSS	NHEK	skin
35	chr17:38803200-38804800	Active TSS	Osteobl	bone
36	chr17:38803200-38805000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:38803200-38805000	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr17:38803200-38805000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:38803200-38805000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:38803200-38805000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr17:38803200-38805000	Active TSS	Aorta	Aorta
42	chr17:38803200-38805000	Active TSS	Fetal Kidney	kidney
43	chr17:38803200-38805000	Active TSS	Lung	lung
44	chr17:38803200-38805200	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr17:38803200-38805200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:38803200-38805200	Active TSS	Esophagus	oesophagus
47	chr17:38803200-38805200	Active TSS	Fetal Intestine Large	intestine
48	chr17:38803200-38805200	Active TSS	Fetal Intestine Small	intestine
49	chr17:38803200-38805400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr17:38803200-38805600	Active TSS	HUES48 Cell Line	embryonic stem cell

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