Variant report

Variant	rs11639369
Chromosome Location	chr15:74494946-74494947
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	RAD21	chr15:74494660-74495837	SK-N-SH_RA	brain:	n/a	chr15:74494901-74494915
2	CTCF	chr15:74494860-74495010	BJ	skin:	n/a	chr15:74494904-74494917
3	EBF1	chr15:74494762-74495021	GM12878	blood:	n/a	chr15:74494886-74494897
4	POLR2A	chr15:74494851-74495264	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr15:74494845-74495707	H1-hESC	embryonic stem cell:	n/a	n/a
6	GABPA	chr15:74494763-74495035	A549	lung:	n/a	n/a
7	TEAD4	chr15:74494944-74495649	H1-hESC	embryonic stem cell:	n/a	n/a
8	EP300	chr15:74494682-74495737	SK-N-SH_RA	brain:	n/a	n/a
9	MAX	chr15:74494663-74495875	H1-hESC	embryonic stem cell:	n/a	chr15:74495240-74495250 chr15:74495165-74495175
10	GABPA	chr15:74494699-74495032	A549	lung:	n/a	n/a
11	CTCF	chr15:74494840-74494990	HepG2	liver:	n/a	chr15:74494904-74494917
12	MAX	chr15:74494739-74495080	K562	blood:	n/a	n/a
13	TFAP2C	chr15:74492581-74495035	Hela-S3	cervix:	n/a	chr15:74493490-74493505 chr15:74492911-74492926
14	UBTF	chr15:74494757-74495033	K562	blood:	n/a	n/a
15	ZBTB7A	chr15:74494946-74495057	K562	blood:	n/a	chr15:74495002-74495009
16	SMARCC1	chr15:74492611-74495990	Hela-S3	cervix:	n/a	n/a
17	SP1	chr15:74494740-74495517	H1-hESC	embryonic stem cell:	n/a	chr15:74495158-74495169 chr15:74495159-74495169 chr15:74495312-74495321 chr15:74495158-74495170 chr15:74495181-74495188 chr15:74495158-74495170 chr15:74495160-74495169 chr15:74495159-74495168 chr15:74495192-74495199 chr15:74495311-74495321 chr15:74495159-74495173
18	TCF12	chr15:74494639-74495911	A549	lung:	n/a	chr15:74495320-74495327
19	CHD1	chr15:74494816-74495126	H1-hESC	embryonic stem cell:	n/a	n/a
20	TCF7L2	chr15:74494730-74495556	HCT-116	colon:	n/a	chr15:74495085-74495099 chr15:74495087-74495096 chr15:74494949-74494956
21	UBTF	chr15:74494850-74495018	K562	blood:	n/a	n/a
22	HDAC2	chr15:74494888-74495258	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZNF143	chr15:74494872-74495514	H1-hESC	embryonic stem cell:	n/a	n/a
24	TCF7L2	chr15:74494239-74495419	HEK293	kidney:	n/a	chr15:74495085-74495099 chr15:74495087-74495096 chr15:74494949-74494956
25	BACH1	chr15:74494893-74495685	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr15:74494909-74495573	H1-hESC	embryonic stem cell:	n/a	n/a
27	ATF2	chr15:74494889-74495592	H1-hESC	embryonic stem cell:	n/a	n/a
28	SP1	chr15:74494593-74495546	A549	lung:	n/a	chr15:74495158-74495169 chr15:74495159-74495169 chr15:74495312-74495321 chr15:74495158-74495170 chr15:74495181-74495188 chr15:74495158-74495170 chr15:74495160-74495169 chr15:74495159-74495168 chr15:74495192-74495199 chr15:74495311-74495321 chr15:74495159-74495173
29	CTCF	chr15:74494880-74495030	BE2_C	brain:	n/a	chr15:74494904-74494917
30	EP300	chr15:74494921-74495506	H1-hESC	embryonic stem cell:	n/a	n/a
31	ELF1	chr15:74494870-74495538	GM12878	blood:	n/a	n/a
32	TAF1	chr15:74494778-74495267	SK-N-SH	brain:	n/a	n/a
33	ZNF263	chr15:74494807-74496849	HEK293-T-REx	kidney:	n/a	chr15:74495716-74495725 chr15:74495068-74495077 chr15:74495251-74495260
34	GATA2	chr15:74494714-74495025	SH-SY5Y	brain:	n/a	n/a
35	TAF1	chr15:74494665-74495084	A549	lung:	n/a	n/a
36	YY1	chr15:74494741-74495577	SK-N-SH_RA	brain:	n/a	chr15:74495455-74495466
37	MAX	chr15:74494534-74495828	A549	lung:	n/a	chr15:74495240-74495250 chr15:74495165-74495175
38	TCF7L2	chr15:74494788-74495313	Hela-S3	cervix:	n/a	chr15:74495085-74495099 chr15:74495087-74495096 chr15:74494949-74494956
39	GABPA	chr15:74494717-74494959	K562	blood:	n/a	n/a
40	TBP	chr15:74494906-74495623	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr15:74494940-74495090	BE2_C	brain:	n/a	n/a
42	GATA3	chr15:74494686-74495990	SK-N-SH	brain:	n/a	n/a
43	CTBP2	chr15:74494460-74495523	H1-hESC	embryonic stem cell:	n/a	n/a
44	TCF12	chr15:74494906-74495375	H1-hESC	embryonic stem cell:	n/a	chr15:74495320-74495327
45	CTCF	chr15:74494820-74494970	SK-N-SH_RA	brain:	n/a	chr15:74494904-74494917
46	POLR2A	chr15:74494680-74495903	SK-N-SH	brain:	n/a	n/a
47	RAD21	chr15:74494665-74495697	H1-hESC	embryonic stem cell:	n/a	chr15:74494901-74494915
48	ZBTB7A	chr15:74494919-74495457	ECC-1	luminal epithelium:	n/a	chr15:74495002-74495009
49	KAP1	chr15:74494824-74495656	U2OS	brain:	n/a	n/a
50	MYC	chr15:74494856-74495737	H1-hESC	embryonic stem cell:	n/a	chr15:74495240-74495250 chr15:74495165-74495175

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:74494909-74494959	Hela-S3	cervix:	n/a
2	chr15:74494909-74494959	SK-N-SH	brain:	n/a
3	chr15:74494909-74494959	LNCaP	prostate:	n/a
4	chr15:74494900-74494950	PFSK-1	brain:	n/a
5	chr15:74494909-74494959	NHBE	bronchial:	n/a
6	chr15:74494900-74494950	K562	blood:	n/a
7	chr15:74494909-74494959	T-47D	breast:	n/a
8	chr15:74494900-74494950	ECC-1	luminal epithelium:	n/a
9	chr15:74494900-74494950	RPTEC	kidney:	n/a
10	chr15:74494900-74494950	AG10803	skin:	n/a
11	chr15:74494900-74494950	U87	brain:	n/a
12	chr15:74494900-74494950	ProgFib	skin:	n/a
13	chr15:74494900-74494950	BE2_C	brain:	n/a
14	chr15:74494909-74494959	Hepatocyte	liver:	n/a
15	chr15:74494900-74494950	HCF	heart:	n/a
16	chr15:74494900-74494950	Hela-S3	cervix:	n/a
17	chr15:74494900-74494950	NHDF-neo	bronchial:	n/a
18	chr15:74494900-74494950	NH-A	brain:	n/a
19	chr15:74494909-74494959	HNPCEpiC	eye:	n/a
20	chr15:74494909-74494959	ProgFib	skin:	n/a
21	chr15:74494900-74494950	HEEpiC	esophagus:	n/a
22	chr15:74494909-74494959	NB4	blood:	n/a
23	chr15:74494900-74494950	GM12891	blood:	n/a
24	chr15:74494900-74494950	GM06990	blood:	n/a
25	chr15:74494909-74494959	A549	lung:	n/a
26	chr15:74494909-74494959	HRPEpiC	eye:	n/a
27	chr15:74494900-74494950	AG04449	skin:	fetal
28	chr15:74494900-74494950	SK-N-SH	brain:	n/a
29	chr15:74494909-74494959	MCF-7	breast:	n/a
30	chr15:74494909-74494959	HL-60	blood:	n/a
31	chr15:74494909-74494959	AG04449	skin:	fetal
32	chr15:74494909-74494959	AG10803	skin:	n/a
33	chr15:74494900-74494950	SKMC	muscle:	n/a
34	chr15:74494909-74494959	HCM	heart:	n/a
35	chr15:74494900-74494950	AoSMC	blood vessel:	n/a
36	chr15:74494900-74494950	GM19239	blood:	n/a
37	chr15:74494909-74494959	GM12892	blood:	n/a
38	chr15:74494900-74494950	HPAEpiC	pulmonary alveolar:	n/a
39	chr15:74494900-74494950	SK-N-SH_RA	brain:	n/a
40	chr15:74494909-74494959	NT2-D1	testis:	n/a
41	chr15:74494909-74494959	GM12891	blood:	n/a
42	chr15:74494900-74494950	AG04450	lung:	fetal
43	chr15:74494909-74494959	HRCEpiC	kidney:	n/a
44	chr15:74494909-74494959	HCF	heart:	n/a
45	chr15:74494900-74494950	T-47D	breast:	n/a
46	chr15:74494900-74494950	PANC-1	pancreas:	n/a
47	chr15:74494900-74494950	HRCEpiC	kidney:	n/a
48	chr15:74494900-74494950	HRE	kidney:	n/a
49	chr15:74494900-74494950	HAEpiC	amniotic membrane:	n/a
50	chr15:74494909-74494959	HRE	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74492912..74495035-chr15:74502031..74504562,2	MCF-7	breast:
2	chr15:74481853..74488513-chr15:74489689..74497281,13	MCF-7	breast:
3	chr15:74494443..74497074-chr15:74501503..74504271,2	K562	blood:
4	chr15:74494408..74497236-chr15:74500706..74502894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259264	TF binding region
STRA6	TF binding region
STRA6	CpG island
ENSG00000259264	CpG island
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11630317	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs11630924	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11631509	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631944	0.82[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11633687	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11639090	0.88[EUR][1000 genomes]
rs11854957	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs11857410	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899173	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905521	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911581	0.81[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12912578	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12913041	0.89[EUR][1000 genomes]
rs12915891	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13259	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs2062309	0.86[EUR][1000 genomes]
rs2415169	0.88[EUR][1000 genomes]
rs2899824	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs34004794	0.81[AMR][1000 genomes]
rs34147822	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34234753	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34573746	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591452	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34868798	0.88[EUR][1000 genomes]
rs34985083	0.81[AMR][1000 genomes]
rs35036456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35255788	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35462746	0.87[EUR][1000 genomes]
rs35661273	0.88[EUR][1000 genomes]
rs35917667	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848160	0.88[EUR][1000 genomes]
rs3848161	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3888004	0.82[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs409856	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs5742915	1.00[CHD][hapmap]
rs62003660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62003661	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62005707	0.88[EUR][1000 genomes]
rs62005709	0.88[EUR][1000 genomes]
rs62005710	0.88[EUR][1000 genomes]
rs62005711	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71399778	0.88[EUR][1000 genomes]
rs7169600	1.00[YRI][hapmap]
rs72747610	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs733163	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8037531	0.87[EUR][1000 genomes]
rs923118	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs9630417	1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs971755	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971756	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971757	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74489200-74509600	Weak transcription	Gastric	stomach
2	chr15:74489400-74499000	Weak transcription	Brain Anterior Caudate	brain
3	chr15:74490600-74496200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:74491000-74503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:74492000-74496800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:74492400-74495000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr15:74492600-74495000	Enhancers	Right Atrium	heart
8	chr15:74492600-74495000	Enhancers	NHDF-Ad	bronchial
9	chr15:74492600-74495400	Flanking Active TSS	Placenta	Placenta
10	chr15:74492600-74495400	Enhancers	Right Ventricle	heart
11	chr15:74492600-74495600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:74492600-74495800	Flanking Active TSS	Hela-S3	cervix
13	chr15:74492600-74496200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:74492600-74496400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:74492600-74496400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:74492600-74496600	Enhancers	HMEC	breast
17	chr15:74492600-74496800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:74492600-74497000	Enhancers	Ovary	ovary
19	chr15:74492600-74497000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:74492600-74497400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:74492600-74497800	Enhancers	GM12878-XiMat	blood
22	chr15:74492600-74498000	Enhancers	Fetal Lung	lung
23	chr15:74492600-74503200	Enhancers	Fetal Muscle Leg	muscle
24	chr15:74492800-74496600	Enhancers	Fetal Heart	heart
25	chr15:74493000-74495000	Enhancers	Fetal Thymus	thymus
26	chr15:74493000-74496800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr15:74493200-74496800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:74493400-74496800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr15:74493400-74498000	Enhancers	NH-A	brain
30	chr15:74493600-74495200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:74493600-74495800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr15:74494000-74496400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:74494000-74497400	Weak transcription	Left Ventricle	heart
34	chr15:74494000-74498400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:74494000-74500200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr15:74494200-74495800	Flanking Active TSS	Fetal Intestine Large	intestine
37	chr15:74494200-74496000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:74494200-74496000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:74494200-74501000	Weak transcription	HSMM	muscle
40	chr15:74494400-74495000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr15:74494400-74495000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
42	chr15:74494400-74495400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:74494400-74495400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:74494400-74497400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:74494400-74498400	Enhancers	Primary hematopoietic stem cells	blood
46	chr15:74494400-74500200	Enhancers	Fetal Brain Male	brain
47	chr15:74494600-74495000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
48	chr15:74494600-74495000	Bivalent Enhancer	HepG2	liver
49	chr15:74494600-74495200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr15:74494600-74495400	Enhancers	Brain Germinal Matrix	brain

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