Variant report

Variant	rs13062516
Chromosome Location	chr3:47021023-47021024
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	MAX	chr3:47020789-47021415	SK-N-SH	brain:	n/a	n/a
2	CBX3	chr3:47020391-47021425	K562	blood:	n/a	n/a
3	HEY1	chr3:47020717-47021500	K562	blood:	n/a	chr3:47021192-47021207 chr3:47021233-47021248 chr3:47021139-47021154
4	POLR2A	chr3:47020814-47021642	NB4	blood:	n/a	n/a
5	POLR2A	chr3:47020495-47021573	K562	blood:	n/a	n/a
6	SP4	chr3:47020652-47021152	H1-hESC	embryonic stem cell:	n/a	chr3:47021056-47021067
7	ZEB1	chr3:47020906-47021625	GM12878	blood:	n/a	n/a
8	EP300	chr3:47021007-47021207	HepG2	liver:	n/a	n/a
9	MAZ	chr3:47020667-47021700	Hela-S3	cervix:	n/a	n/a
10	RFX5	chr3:47020996-47021090	K562	blood:	n/a	n/a
11	MXI1	chr3:47020475-47021913	IMR90	lung:	n/a	n/a
12	ZNF143	chr3:47020642-47021465	K562	blood:	n/a	n/a
13	ZBTB7A	chr3:47020652-47021283	ECC-1	luminal epithelium:	n/a	chr3:47020877-47020884
14	RCOR1	chr3:47020556-47021805	K562	blood:	n/a	n/a
15	MYC	chr3:47020971-47021571	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:47020872-47021448	A549	lung:	n/a	n/a
17	EP300	chr3:47020626-47021433	SK-N-SH	brain:	n/a	chr3:47021290-47021299
18	JUND	chr3:47020889-47021322	HepG2	liver:	n/a	chr3:47021289-47021298 chr3:47021105-47021114
19	RUNX3	chr3:47020651-47021458	GM12878	blood:	n/a	n/a
20	UBTF	chr3:47020623-47021834	K562	blood:	n/a	n/a
21	SMC3	chr3:47020920-47021377	Hela-S3	cervix:	n/a	n/a
22	ETS1	chr3:47020875-47021601	K562	blood:	n/a	chr3:47021288-47021299 chr3:47021107-47021118
23	POLR2A	chr3:47020806-47021492	K562	blood:	n/a	n/a
24	RCOR1	chr3:47020401-47021544	IMR90	lung:	n/a	n/a
25	YY1	chr3:47020592-47021499	H1-hESC	embryonic stem cell:	n/a	chr3:47020665-47020676 chr3:47021013-47021024 chr3:47020871-47020880 chr3:47021143-47021152 chr3:47021109-47021123 chr3:47021107-47021118 chr3:47021293-47021302
26	YY1	chr3:47020682-47021449	ECC-1	luminal epithelium:	n/a	chr3:47021013-47021024 chr3:47020871-47020880 chr3:47021143-47021152 chr3:47021109-47021123 chr3:47021107-47021118 chr3:47021293-47021302
27	EGR1	chr3:47020976-47021410	K562	blood:	n/a	chr3:47021300-47021314
28	MTA3	chr3:47020405-47021221	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:47020714-47021464	K562	blood:	n/a	n/a
30	SIN3AK20	chr3:47020787-47021618	PANC-1	pancreas:	n/a	n/a
31	YY1	chr3:47020729-47021390	SK-N-SH_RA	brain:	n/a	chr3:47021013-47021024 chr3:47020871-47020880 chr3:47021143-47021152 chr3:47021109-47021123 chr3:47021107-47021118 chr3:47021293-47021302
32	POLR2A	chr3:47020624-47021414	U87	brain:	n/a	n/a
33	TBL1XR1	chr3:47020851-47021392	K562	blood:	n/a	n/a
34	MAX	chr3:47020395-47021897	A549	lung:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
35	RAD21	chr3:47020895-47021379	HepG2	liver:	n/a	n/a
36	TBP	chr3:47020846-47021336	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:47020731-47021571	HL-60	blood:	n/a	n/a
38	CHD2	chr3:47020819-47021244	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF3	chr3:47021012-47021652	GM12878	blood:	n/a	chr3:47021313-47021323 chr3:47021308-47021321
40	HA-E2F1	chr3:47020589-47021847	MCF-7	breast:	n/a	chr3:47020871-47020880 chr3:47020710-47020722 chr3:47020890-47020901 chr3:47021293-47021302 chr3:47021236-47021245
41	MAX	chr3:47020656-47021375	K562	blood:	n/a	n/a
42	POLR2A	chr3:47020735-47021374	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr3:47020748-47021561	HUVEC	blood vessel:	n/a	n/a
44	CTCF	chr3:47020898-47021409	H1-hESC	embryonic stem cell:	n/a	chr3:47021287-47021300
45	POLR2A	chr3:47020829-47021123	GM12891	blood:	n/a	n/a
46	POLR2A	chr3:47020688-47021680	GM12891	blood:	n/a	n/a
47	MAZ	chr3:47020928-47021675	HepG2	liver:	n/a	n/a
48	E2F6	chr3:47020481-47021673	K562	blood:	n/a	chr3:47020871-47020880 chr3:47020710-47020722 chr3:47020890-47020901 chr3:47021316-47021328 chr3:47021293-47021302 chr3:47021236-47021245
49	POLR2A	chr3:47020642-47021738	GM18505	blood:	n/a	n/a
50	TAF1	chr3:47020827-47021347	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:47020973-47021023	SKMC	muscle:	n/a
2	chr3:47020973-47021023	GM12891	blood:	n/a
3	chr3:47020973-47021023	Jurkat	blood:	n/a
4	chr3:47020973-47021023	NH-A	brain:	n/a
5	chr3:47020973-47021023	ovcar-3	ovarian:	n/a
6	chr3:47020973-47021023	CMK	blood:	n/a
7	chr3:47020973-47021023	ECC-1	luminal epithelium:	n/a
8	chr3:47020973-47021023	HEK293	kidney:	embryo
9	chr3:47020973-47021023	HepG2	liver:	n/a
10	chr3:47020973-47021023	HCM	heart:	n/a
11	chr3:47020973-47021023	IMR90	lung:	fetal
12	chr3:47020973-47021023	SK-N-MC	brain:	n/a
13	chr3:47020973-47021023	MCF-7	breast:	n/a
14	chr3:47020973-47021023	K562	blood:	n/a
15	chr3:47020973-47021023	NB4	blood:	n/a
16	chr3:47020973-47021023	HCPEpiC	choroid plexus:	n/a
17	chr3:47020973-47021023	GM06990	blood:	n/a
18	chr3:47020973-47021023	Caco-2	colon:	n/a
19	chr3:47020973-47021023	PANC-1	pancreas:	n/a
20	chr3:47020973-47021023	AG04449	skin:	fetal
21	chr3:47020973-47021023	HNPCEpiC	eye:	n/a
22	chr3:47020973-47021023	HRE	kidney:	n/a
23	chr3:47020973-47021023	AG09309	skin:	n/a
24	chr3:47020973-47021023	RPTEC	kidney:	n/a
25	chr3:47020973-47021023	GM12892	blood:	n/a
26	chr3:47020973-47021023	HPAEpiC	pulmonary alveolar:	n/a
27	chr3:47020973-47021023	NHBE	bronchial:	n/a
28	chr3:47020973-47021023	AG04450	lung:	fetal
29	chr3:47020973-47021023	AG09319	gingival:	n/a
30	chr3:47020973-47021023	HEEpiC	esophagus:	n/a
31	chr3:47020973-47021023	HCT-116	colon:	n/a
32	chr3:47020973-47021023	LNCaP	prostate:	n/a
33	chr3:47020973-47021023	HCF	heart:	n/a
34	chr3:47020973-47021023	MCF10A-Er-Src	breast:	n/a
35	chr3:47020973-47021023	H1-hESC	embryonic stem cell:	embryo
36	chr3:47020973-47021023	HAEpiC	amniotic membrane:	n/a
37	chr3:47020973-47021023	BE2_C	brain:	n/a
38	chr3:47020973-47021023	Hela-S3	cervix:	n/a
39	chr3:47020973-47021023	SK-N-SH	brain:	n/a
40	chr3:47020973-47021023	U87	brain:	n/a
41	chr3:47020973-47021023	GM19239	blood:	n/a
42	chr3:47020973-47021023	SK-N-SH_RA	brain:	n/a
43	chr3:47020973-47021023	GM12878	blood:	n/a
44	chr3:47020973-47021023	PrEC	prostate:	n/a
45	chr3:47020973-47021023	BJ	skin:	n/a
46	chr3:47020973-47021023	HIPEpiC	eye:	n/a
47	chr3:47020973-47021023	AG10803	skin:	n/a
48	chr3:47020973-47021023	NT2-D1	testis:	n/a
49	chr3:47020973-47021023	HUVEC	blood vessel:	n/a
50	chr3:47020973-47021023	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47020574..47023054-chr3:47051075..47053218,2	MCF-7	breast:
2	chr3:47019689..47022693-chr3:47040941..47043835,3	MCF-7	breast:
3	chr3:47019697..47022640-chr3:47324324..47326151,2	K562	blood:

Variant related genes	Relation type
CCDC12	TF binding region
NBEAL2	TF binding region
CCDC12	CpG island
NBEAL2	CpG island
ENSG00000114648	Chromatin interaction
ENSG00000236409	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11130109	0.89[AFR][1000 genomes]
rs11706212	0.96[AFR][1000 genomes]
rs11709876	0.94[AFR][1000 genomes]
rs11713537	0.81[AFR][1000 genomes]
rs12487763	0.84[AFR][1000 genomes]
rs13062185	0.97[AFR][1000 genomes]
rs13074884	0.81[AFR][1000 genomes]
rs13079416	0.90[AFR][1000 genomes]
rs13082531	0.96[AFR][1000 genomes]
rs1463394	0.89[AFR][1000 genomes]
rs1473382	0.88[AFR][1000 genomes]
rs1563431	0.82[AFR][1000 genomes]
rs1814564	0.82[AFR][1000 genomes]
rs1869870	0.85[AFR][1000 genomes]
rs2124510	0.95[AFR][1000 genomes]
rs2385868	0.94[AFR][1000 genomes]
rs2385872	0.84[AFR][1000 genomes]
rs2891893	0.89[AFR][1000 genomes]
rs4324490	0.94[AFR][1000 genomes]
rs4378998	0.94[AFR][1000 genomes]
rs4389512	0.94[AFR][1000 genomes]
rs4450857	0.84[AFR][1000 genomes]
rs4478107	0.82[AFR][1000 genomes]
rs4522803	0.88[AFR][1000 genomes]
rs4543047	0.94[AFR][1000 genomes]
rs4682832	0.90[AFR][1000 genomes]
rs4682833	0.86[AFR][1000 genomes]
rs4682834	0.82[AFR][1000 genomes]
rs4682835	0.89[AFR][1000 genomes]
rs4682836	0.89[AFR][1000 genomes]
rs4682838	0.82[AFR][1000 genomes]
rs4683279	0.90[AFR][1000 genomes]
rs4683285	0.88[AFR][1000 genomes]
rs6442043	0.82[AFR][1000 genomes]
rs6442044	0.89[AFR][1000 genomes]
rs6442047	0.94[AFR][1000 genomes]
rs6442048	0.95[AFR][1000 genomes]
rs6442050	0.82[AFR][1000 genomes]
rs6766676	0.89[AFR][1000 genomes]
rs6806521	0.94[AFR][1000 genomes]
rs6809904	0.87[AFR][1000 genomes]
rs7624549	0.89[AFR][1000 genomes]
rs7625011	0.94[AFR][1000 genomes]
rs7630904	0.80[AFR][1000 genomes]
rs7643868	0.90[AFR][1000 genomes]
rs7646076	0.88[AFR][1000 genomes]
rs7649941	0.89[AFR][1000 genomes]
rs936177	0.87[AFR][1000 genomes]
rs936178	0.84[AFR][1000 genomes]
rs936179	0.82[AFR][1000 genomes]
rs936180	0.88[AFR][1000 genomes]
rs936181	0.97[AFR][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	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
8	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases
11	esv3359860	chr3:47019973-47022521	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47020200-47021600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:47020200-47021800	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:47020400-47021200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:47020400-47021600	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr3:47020400-47021600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:47020400-47021600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:47020400-47021600	Active TSS	Brain Germinal Matrix	brain
8	chr3:47020400-47021800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:47020400-47021800	Active TSS	H9 Cell Line	embryonic stem cell
10	chr3:47020400-47021800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:47020400-47021800	Active TSS	Esophagus	oesophagus
12	chr3:47020400-47021800	Active TSS	Pancreas	Pancrea
13	chr3:47020400-47021800	Active TSS	Psoas Muscle	Psoas
14	chr3:47020400-47022000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:47020400-47022000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:47020400-47022000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:47020400-47022200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:47020400-47022200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:47020400-47022400	Active TSS	Fetal Kidney	kidney
20	chr3:47020400-47022600	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr3:47020400-47022600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr3:47020600-47021600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:47020600-47021600	Active TSS	Brain Angular Gyrus	brain
24	chr3:47020600-47021600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:47020600-47021600	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:47020600-47021600	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr3:47020600-47021600	Active TSS	Thymus	Thymus
28	chr3:47020600-47021800	Active TSS	Lung	lung
29	chr3:47020600-47021800	Active TSS	Small Intestine	intestine
30	chr3:47020600-47021800	Active TSS	HSMMtube	muscle
31	chr3:47020600-47022000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr3:47020600-47022000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:47020600-47022000	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr3:47020600-47022000	Active TSS	Aorta	Aorta
35	chr3:47020600-47022000	Active TSS	Colon Smooth Muscle	Colon
36	chr3:47020600-47022000	Active TSS	HSMM	muscle
37	chr3:47020600-47022200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:47020600-47022200	Active TSS	Left Ventricle	heart
39	chr3:47020600-47022200	Active TSS	Right Atrium	heart
40	chr3:47020600-47022400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:47020600-47022600	Flanking Active TSS	HMEC	breast
42	chr3:47020600-47023800	Active TSS	Rectal Smooth Muscle	rectum
43	chr3:47020800-47021200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:47020800-47021600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr3:47020800-47021600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:47020800-47021600	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr3:47020800-47021600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:47020800-47021600	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr3:47020800-47021600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:47020800-47021600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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