Variant report

Variant	rs11632120
Chromosome Location	chr15:43415373-43415374
allele	C/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	CTCF	chr15:43415340-43415490	GM12873	blood:	n/a	n/a
2	ZNF384	chr15:43415361-43416262	K562	blood:	n/a	n/a
3	JUND	chr15:43415011-43415740	K562	blood:	n/a	n/a
4	SIN3A	chr15:43415317-43415516	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:43414750-43415841	H1-neurons	neurons:	n/a	n/a
6	RCOR1	chr15:43414173-43415743	K562	blood:	n/a	n/a
7	SRF	chr15:43415213-43415836	ECC-1	luminal epithelium:	n/a	chr15:43415527-43415544 chr15:43415528-43415543 chr15:43415526-43415544 chr15:43415526-43415540 chr15:43415524-43415541 chr15:43415529-43415542
8	SRF	chr15:43415332-43415649	H1-hESC	embryonic stem cell:	n/a	chr15:43415527-43415544 chr15:43415528-43415543 chr15:43415526-43415544 chr15:43415526-43415540 chr15:43415524-43415541 chr15:43415529-43415542
9	ZMIZ1	chr15:43415025-43415734	K562	blood:	n/a	n/a
10	MAX	chr15:43415339-43415514	HepG2	liver:	n/a	chr15:43415363-43415372
11	POLR2A	chr15:43415258-43415808	GM12878	blood:	n/a	n/a
12	RUNX3	chr15:43414987-43415601	GM12878	blood:	n/a	n/a
13	STAT3	chr15:43415293-43415595	MCF10A-Er-Src	breast:	n/a	chr15:43415404-43415416
14	NRF1	chr15:43415193-43415600	GM12878	blood:	n/a	n/a
15	CBX3	chr15:43414798-43415815	K562	blood:	n/a	n/a
16	NR2F2	chr15:43414146-43415717	K562	blood:	n/a	n/a
17	EP300	chr15:43415159-43415576	GM12878	blood:	n/a	n/a
18	TEAD4	chr15:43414928-43415693	K562	blood:	n/a	n/a
19	ZNF143	chr15:43415313-43415574	GM12878	blood:	n/a	n/a
20	CHD2	chr15:43415294-43415725	GM12878	blood:	n/a	n/a
21	MAX	chr15:43414748-43415749	K562	blood:	n/a	chr15:43415363-43415372
22	CTCF	chr15:43415340-43415490	GM06990	blood:	n/a	n/a
23	HEY1	chr15:43415138-43415780	K562	blood:	n/a	n/a
24	ARID3A	chr15:43414883-43415411	HepG2	liver:	n/a	n/a
25	MXI1	chr15:43415183-43415557	K562	blood:	n/a	chr15:43415357-43415372
26	YY1	chr15:43415229-43415677	K562	blood:	n/a	n/a
27	HCFC1	chr15:43415121-43415788	K562	blood:	n/a	n/a
28	EGR1	chr15:43415282-43415477	GM12878	blood:	n/a	n/a
29	SRF	chr15:43415365-43415725	H1-hESC	embryonic stem cell:	n/a	chr15:43415527-43415544 chr15:43415528-43415543 chr15:43415526-43415544 chr15:43415526-43415540 chr15:43415524-43415541 chr15:43415529-43415542
30	UBTF	chr15:43415291-43415637	K562	blood:	n/a	n/a
31	POLR2A	chr15:43414333-43415798	PBDE	blood:	n/a	n/a
32	WRNIP1	chr15:43415256-43415638	GM12878	blood:	n/a	n/a
33	SRF	chr15:43415245-43415751	ECC-1	luminal epithelium:	n/a	chr15:43415527-43415544 chr15:43415528-43415543 chr15:43415526-43415544 chr15:43415526-43415540 chr15:43415524-43415541 chr15:43415529-43415542
34	SMC3	chr15:43414968-43415684	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr15:43414950-43415700	H1-neurons	neurons:	n/a	n/a
36	SIN3AK20	chr15:43415200-43415481	HepG2	liver:	n/a	n/a
37	MAX	chr15:43415121-43415728	ECC-1	luminal epithelium:	n/a	chr15:43415363-43415372
38	CTCF	chr15:43415360-43415510	AoAF	blood vessel:	n/a	chr15:43415490-43415503
39	POLR2A	chr15:43415340-43415667	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr15:43414722-43415654	HepG2	liver:	n/a	chr15:43415357-43415372
41	POLR2A	chr15:43415107-43415665	HCT-116	colon:	n/a	n/a
42	MYC	chr15:43415212-43415732	K562	blood:	n/a	chr15:43415363-43415372
43	POLR2A	chr15:43415232-43415629	GM12878	blood:	n/a	n/a
44	CTCF	chr15:43415360-43415510	GM12868	blood:	n/a	chr15:43415490-43415503
45	POLR2A	chr15:43415203-43415727	HUVEC	blood vessel:	n/a	n/a
46	SRF	chr15:43415355-43415672	GM12878	blood:	n/a	chr15:43415527-43415544 chr15:43415528-43415543 chr15:43415526-43415544 chr15:43415526-43415540 chr15:43415524-43415541 chr15:43415529-43415542
47	POLR2A	chr15:43415219-43415691	Gliobla	brain:	n/a	n/a
48	ZNF143	chr15:43414822-43415524	Hela-S3	cervix:	n/a	n/a
49	MYC	chr15:43415334-43415546	MCF10A-Er-Src	breast:	n/a	chr15:43415363-43415372
50	RFX5	chr15:43415143-43415688	Hela-S3	cervix:	n/a	chr15:43415358-43415373 chr15:43415358-43415373 chr15:43415358-43415373

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:43415332-43415382	NHBE	bronchial:	n/a
2	chr15:43415332-43415382	HepG2	liver:	n/a
3	chr15:43415332-43415382	LNCaP	prostate:	n/a
4	chr15:43415332-43415382	HEEpiC	esophagus:	n/a
5	chr15:43415332-43415382	HRPEpiC	eye:	n/a
6	chr15:43415332-43415382	NB4	blood:	n/a
7	chr15:43415332-43415382	Caco-2	colon:	n/a
8	chr15:43415332-43415382	BE2_C	brain:	n/a
9	chr15:43415332-43415382	MCF-7	breast:	n/a
10	chr15:43415332-43415382	AG10803	skin:	n/a
11	chr15:43415332-43415382	GM19239	blood:	n/a
12	chr15:43415332-43415382	HCPEpiC	choroid plexus:	n/a
13	chr15:43415332-43415382	AG04450	lung:	fetal
14	chr15:43415332-43415382	HCT-116	colon:	n/a
15	chr15:43415332-43415382	SK-N-SH_RA	brain:	n/a
16	chr15:43415332-43415382	AG09309	skin:	n/a
17	chr15:43415332-43415382	HUVEC	blood vessel:	n/a
18	chr15:43415332-43415382	GM12892	blood:	n/a
19	chr15:43415332-43415382	GM12891	blood:	n/a
20	chr15:43415332-43415382	PANC-1	pancreas:	n/a
21	chr15:43415332-43415382	AoSMC	blood vessel:	n/a
22	chr15:43415332-43415382	NT2-D1	testis:	n/a
23	chr15:43415332-43415382	ProgFib	skin:	n/a
24	chr15:43415332-43415382	A549	lung:	n/a
25	chr15:43415332-43415382	HIPEpiC	eye:	n/a
26	chr15:43415332-43415382	T-47D	breast:	n/a
27	chr15:43415332-43415382	HL-60	blood:	n/a
28	chr15:43415332-43415382	SK-N-MC	brain:	n/a
29	chr15:43415332-43415382	AG04449	skin:	fetal
30	chr15:43415332-43415382	BJ	skin:	n/a
31	chr15:43415332-43415382	SKMC	muscle:	n/a
32	chr15:43415332-43415382	U87	brain:	n/a
33	chr15:43415332-43415382	NHDF-neo	bronchial:	n/a
34	chr15:43415332-43415382	K562	blood:	n/a
35	chr15:43415332-43415382	PrEC	prostate:	n/a
36	chr15:43415332-43415382	HPAEpiC	pulmonary alveolar:	n/a
37	chr15:43415332-43415382	HCM	heart:	n/a
38	chr15:43415332-43415382	HMEC	breast:	n/a
39	chr15:43415332-43415382	SK-N-SH	brain:	n/a
40	chr15:43415332-43415382	HCF	heart:	n/a
41	chr15:43415332-43415382	NH-A	brain:	n/a
42	chr15:43415332-43415382	GM06990	blood:	n/a
43	chr15:43415332-43415382	Hepatocyte	liver:	n/a
44	chr15:43415332-43415382	H1-hESC	embryonic stem cell:	embryo
45	chr15:43415332-43415382	Jurkat	blood:	n/a
46	chr15:43415332-43415382	AG09319	gingival:	n/a
47	chr15:43415332-43415382	MCF10A-Er-Src	breast:	n/a
48	chr15:43415332-43415382	ECC-1	luminal epithelium:	n/a
49	chr15:43415332-43415382	PFSK-1	brain:	n/a
50	chr15:43415332-43415382	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:43412581..43417001-chr15:43422670..43429913,10	K562	blood:
2	chr15:43397628..43400398-chr15:43414771..43418048,4	MCF-7	breast:
3	chr15:43413837..43416869-chr15:43476770..43480897,4	K562	blood:
4	chr15:43411554..43416767-chr15:43424269..43426823,6	K562	blood:
5	chr15:43414543..43416437-chr15:43476770..43479731,2	K562	blood:
6	chr15:43414412..43417295-chr15:43437126..43440064,2	K562	blood:

Variant related genes	Relation type
TMEM62	TF binding region
TMEM62	CpG island
ENSG00000137842	Chromatin interaction
ENSG00000166946	Chromatin interaction
ENSG00000261687	Chromatin interaction
ENSG00000260928	Chromatin interaction
ENSG00000159459	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10851414	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070389	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11070390	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11629629	0.87[AFR][1000 genomes]
rs12442190	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913112	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12913134	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1474200	0.91[CHB][hapmap];0.96[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs2056346	0.91[CHB][hapmap];0.96[JPT][hapmap];0.83[ASN][1000 genomes]
rs2139651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2139652	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277532	0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs476342	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489964	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4923956	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs502157	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs525403	0.86[CHB][hapmap]
rs530118	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs574531	0.81[ASN][1000 genomes]
rs574856	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7165861	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166467	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8026333	1.00[YRI][hapmap]
rs9635327	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	esv1802035	chr15:43370916-43487742	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11632120	CCNDBP1	cis	multi-tissue	Pritchard
rs11632120	TGM5	cis	Lymphoblastoid	GTEx
rs11632120	CCNDBP1	cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43414400-43415800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:43414400-43415800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr15:43414600-43415400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr15:43414600-43415400	Active TSS	Fetal Stomach	stomach
5	chr15:43414600-43415800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr15:43414600-43415800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:43414600-43415800	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr15:43414600-43415800	Active TSS	Right Ventricle	heart
9	chr15:43414600-43415800	Flanking Active TSS	NHEK	skin
10	chr15:43414600-43415800	Active TSS	NHLF	lung
11	chr15:43414800-43415400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:43414800-43415400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr15:43414800-43415400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr15:43414800-43415400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr15:43414800-43415400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:43414800-43415400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:43414800-43415400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:43414800-43415400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:43414800-43415400	Flanking Active TSS	Liver	Liver
20	chr15:43414800-43415600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr15:43414800-43415600	Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr15:43414800-43415600	Active TSS	Esophagus	oesophagus
23	chr15:43414800-43415600	Active TSS	Osteobl	bone
24	chr15:43414800-43415800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:43414800-43415800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:43414800-43415800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:43414800-43415800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr15:43414800-43415800	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr15:43414800-43415800	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr15:43414800-43415800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr15:43414800-43415800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr15:43414800-43415800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr15:43414800-43415800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr15:43414800-43415800	Active TSS	Aorta	Aorta
35	chr15:43414800-43415800	Active TSS	Brain Angular Gyrus	brain
36	chr15:43414800-43415800	Active TSS	Brain Germinal Matrix	brain
37	chr15:43414800-43415800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr15:43414800-43415800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:43414800-43415800	Active TSS	Brain Substantia Nigra	brain
40	chr15:43414800-43415800	Flanking Active TSS	Fetal Brain Male	brain
41	chr15:43414800-43415800	Active TSS	Fetal Brain Female	brain
42	chr15:43414800-43415800	Active TSS	Fetal Intestine Large	intestine
43	chr15:43414800-43415800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr15:43414800-43415800	Active TSS	Left Ventricle	heart
45	chr15:43414800-43415800	Active TSS	Psoas Muscle	Psoas
46	chr15:43414800-43415800	Active TSS	Right Atrium	heart
47	chr15:43414800-43415800	Flanking Active TSS	Dnd41	blood
48	chr15:43414800-43415800	Flanking Active TSS	HUVEC	blood vessel
49	chr15:43414800-43416000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:43414800-43416000	Active TSS	Stomach Smooth Muscle	stomach

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