Variant report

Variant	rs3806915
Chromosome Location	chr5:115911916-115911917
allele	G/T
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	CTCF	chr5:115911713-115912040	A549	lung:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
2	CTCF	chr5:115911880-115912030	GM12870	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
3	ZEB1	chr5:115911709-115912409	GM12878	blood:	n/a	n/a
4	RAD21	chr5:115911711-115912093	HepG2	liver:	n/a	chr5:115911934-115911953
5	RAD21	chr5:115911764-115912132	IMR90	lung:	n/a	chr5:115911934-115911953
6	FOS	chr5:115910987-115912085	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr5:115911779-115911981	MCF10A-Er-Src	breast:	n/a	n/a
8	SMC3	chr5:115911810-115912044	Hela-S3	cervix:	n/a	chr5:115911939-115911949
9	CTCF	chr5:115911775-115912122	K562	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
10	CTCF	chr5:115911781-115912106	GM12892	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
11	RAD21	chr5:115911532-115912310	HCT-116	colon:	n/a	chr5:115911934-115911953
12	YY1	chr5:115911726-115912293	GM12878	blood:	n/a	n/a
13	CTCF	chr5:115911840-115911990	HMEC	breast:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
14	CTCF	chr5:115911840-115911990	HRE	kidney:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
15	RAD21	chr5:115911734-115912053	HepG2	liver:	n/a	chr5:115911934-115911953
16	CTCF	chr5:115911860-115912010	Hela-S3	cervix:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
17	TBP	chr5:115910295-115912307	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr5:115911860-115912010	HBMEC	blood vessel:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
19	CTCF	chr5:115911775-115912108	GM19238	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
20	CTCF	chr5:115911840-115911990	NHEK	skin:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
21	CTCF	chr5:115911840-115911990	AoAF	blood vessel:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
22	STAT5A	chr5:115911642-115912499	GM12878	blood:	n/a	n/a
23	CTCF	chr5:115911860-115912010	RPTEC	kidney:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
24	CTCF	chr5:115911806-115912065	K562	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
25	POLR2A	chr5:115911135-115912558	H1-hESC	embryonic stem cell:	n/a	n/a
26	YY1	chr5:115911777-115912028	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr5:115911840-115911990	SAEC	small airway:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
28	SMC3	chr5:115911817-115912089	K562	blood:	n/a	chr5:115911939-115911949
29	CTCF	chr5:115911751-115912076	T-47D	breast:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
30	CTCF	chr5:115911880-115912030	GM12869	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
31	E2F6	chr5:115911652-115912554	H1-hESC	embryonic stem cell:	n/a	chr5:115912374-115912383 chr5:115912021-115912031 chr5:115912093-115912100 chr5:115911997-115912006 chr5:115912093-115912100 chr5:115912093-115912100
32	EP300	chr5:115911664-115913404	GM12878	blood:	n/a	n/a
33	CTCF	chr5:115911860-115912010	HMEC	breast:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
34	CTCF	chr5:115911880-115912030	BE2_C	brain:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
35	FOXM1	chr5:115911626-115912214	GM12878	blood:	n/a	n/a
36	NRF1	chr5:115911692-115912120	H1-hESC	embryonic stem cell:	n/a	chr5:115911997-115912006
37	CTCF	chr5:115911860-115912010	NHDF-neo	bronchial:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
38	MAZ	chr5:115911774-115912042	HepG2	liver:	n/a	n/a
39	CTCF	chr5:115911880-115912030	HRPEpiC	eye:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
40	RAD21	chr5:115911664-115912192	ECC-1	luminal epithelium:	n/a	chr5:115911934-115911953
41	BRCA1	chr5:115911336-115912586	H1-hESC	embryonic stem cell:	n/a	n/a
42	CHD2	chr5:115911292-115913493	GM12878	blood:	n/a	n/a
43	CTCF	chr5:115911880-115912030	MCF-7	breast:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
44	CTCF	chr5:115911741-115912117	K562	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
45	SMC3	chr5:115911739-115912100	HepG2	liver:	n/a	chr5:115911939-115911949
46	CTCF	chr5:115911880-115912030	GM06990	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
47	CTCF	chr5:115911816-115912032	A549	lung:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
48	CTCF	chr5:115911860-115912010	WI-38	lung:	n/a	chr5:115911936-115911949 chr5:115911933-115911951
49	BHLHE40	chr5:115911151-115912351	GM12878	blood:	n/a	n/a
50	CTCF	chr5:115911807-115912093	GM12891	blood:	n/a	chr5:115911936-115911949 chr5:115911933-115911951

No.	Distal block	Cell Line	Cell type
1	chr5:115911320..115912473-chr5:116283341..116284236,4	MCF-7	breast:
2	chr5:115904366..115906105-chr5:115910810..115912566,2	K562	blood:
3	chr5:115911257..115912668-chr5:116283296..116284268,6	MCF-7	breast:

Variant related genes	Relation type
SEMA6A	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10045872	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10053792	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10061055	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10062998	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10066922	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10067680	0.93[EUR][1000 genomes]
rs10070276	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10073289	0.84[ASN][1000 genomes]
rs10074788	0.97[ASN][1000 genomes]
rs10075410	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10076201	0.95[EUR][1000 genomes]
rs10080023	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1027742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11953558	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12719220	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13354122	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13355655	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13357599	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13360587	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1345706	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1345707	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17140120	0.81[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs17140171	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140176	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17140192	0.93[EUR][1000 genomes]
rs1862372	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1862373	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2840113	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28489253	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3806914	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806916	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56257700	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57497884	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57557217	0.97[ASN][1000 genomes]
rs58364462	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59351578	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs60783407	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs686664	0.93[EUR][1000 genomes]
rs6878936	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6897765	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6898172	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73780374	0.85[ASN][1000 genomes]
rs73780375	0.85[ASN][1000 genomes]
rs9327010	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327011	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327012	0.93[ASN][1000 genomes]

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115906000-115912400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:115906400-115912200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr5:115906400-115912400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:115906800-115912600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:115906800-115912800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:115907000-115912200	Active TSS	Fetal Intestine Large	intestine
7	chr5:115907000-115912400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:115907200-115912200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr5:115907200-115912600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:115907200-115912600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:115907400-115912200	Active TSS	Fetal Intestine Small	intestine
12	chr5:115907400-115912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr5:115907400-115912600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:115907400-115912600	Active TSS	Brain Angular Gyrus	brain
15	chr5:115907600-115912000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr5:115907600-115912400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:115907600-115912400	Active TSS	Ovary	ovary
18	chr5:115907600-115912600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:115907600-115912600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:115907600-115912600	Active TSS	Brain Anterior Caudate	brain
21	chr5:115907600-115912600	Active TSS	Brain Cingulate Gyrus	brain
22	chr5:115907600-115912600	Active TSS	Brain Substantia Nigra	brain
23	chr5:115907800-115912600	Active TSS	Fetal Kidney	kidney
24	chr5:115908000-115912400	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr5:115908000-115912400	Bivalent/Poised TSS	Thymus	Thymus
26	chr5:115908000-115912600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:115908200-115912400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr5:115908200-115912400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:115908200-115912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr5:115908400-115912000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
31	chr5:115908400-115912400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr5:115908400-115912400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:115908400-115912600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr5:115909000-115912400	Active TSS	Stomach Smooth Muscle	stomach
35	chr5:115909200-115912600	Active TSS	Right Atrium	heart
36	chr5:115909400-115912000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr5:115909400-115912800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr5:115909600-115912200	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr5:115909600-115912400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr5:115909600-115912400	Active TSS	Rectal Smooth Muscle	rectum
41	chr5:115909600-115912400	Active TSS	Small Intestine	intestine
42	chr5:115909800-115912400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:115909800-115912400	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr5:115909800-115912400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:115909800-115912600	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr5:115909800-115912600	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr5:115910000-115912200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:115910000-115912200	Active TSS	Esophagus	oesophagus
49	chr5:115910000-115912200	Active TSS	Fetal Muscle Trunk	muscle
50	chr5:115910000-115912200	Active TSS	Pancreas	Pancrea

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