Variant report

Variant	rs6438533
Chromosome Location	chr3:119216714-119216715
allele	C/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	MTA3	chr3:119215802-119218062	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:119216660-119216972	Hela-S3	cervix:	n/a	n/a
3	SIN3AK20	chr3:119216517-119217982	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:119216636-119217820	GM18505	blood:	n/a	n/a
5	POLR2A	chr3:119215414-119217916	K562	blood:	n/a	n/a
6	POLR2A	chr3:119216642-119216756	HUVEC	blood vessel:	n/a	n/a
7	STAT5A	chr3:119216631-119217934	GM12878	blood:	n/a	chr3:119217384-119217391 chr3:119217712-119217736 chr3:119217398-119217405
8	POLR2A	chr3:119216604-119217916	Raji	blood:	n/a	n/a
9	MAFK	chr3:119216542-119216854	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:119216562-119217905	PANC-1	pancreas:	n/a	n/a
11	EP300	chr3:119216669-119216764	GM12878	blood:	n/a	n/a
12	GABPA	chr3:119216469-119218222	MCF-7	breast:	n/a	chr3:119217351-119217360
13	POLR2A	chr3:119216045-119217915	GM12892	blood:	n/a	n/a
14	MXI1	chr3:119216595-119217874	HepG2	liver:	n/a	n/a
15	MAFK	chr3:119216560-119216844	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:119216516-119218683	K562	blood:	n/a	n/a
17	GABPA	chr3:119216646-119217919	SK-N-SH	brain:	n/a	chr3:119217351-119217360
18	POLR2A	chr3:119216039-119216895	U87	brain:	n/a	n/a
19	POLR2A	chr3:119216115-119217972	GM12891	blood:	n/a	n/a
20	MAX	chr3:119216704-119217885	NB4	blood:	n/a	n/a
21	MAZ	chr3:119216688-119217769	K562	blood:	n/a	n/a
22	MAX	chr3:119216694-119217864	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr3:119216562-119217898	ProgFib	skin:	n/a	n/a
24	POLR2A	chr3:119216646-119217000	GM12878	blood:	n/a	n/a
25	ELF1	chr3:119216625-119217914	MCF-7	breast:	n/a	chr3:119217315-119217326 chr3:119217271-119217280 chr3:119217270-119217281 chr3:119217270-119217281 chr3:119217313-119217326 chr3:119217316-119217325
26	POLR2A	chr3:119216648-119217812	IMR90	lung:	n/a	n/a
27	MYC	chr3:119216625-119217776	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr3:119216492-119218065	H1-hESC	embryonic stem cell:	n/a	n/a
29	REST	chr3:119216594-119218166	H1-neurons	neurons:	n/a	chr3:119217828-119217841
30	POLR2A	chr3:119216239-119217945	HepG2	liver:	n/a	n/a
31	MXI1	chr3:119216044-119220289	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr3:119216678-119216971	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr3:119216409-119217948	PBDE	blood:	n/a	n/a
34	POLR2A	chr3:119216528-119217908	HCT-116	colon:	n/a	n/a
35	GABPA	chr3:119216627-119217921	MCF-7	breast:	n/a	chr3:119217351-119217360
36	PML	chr3:119216632-119217823	GM12878	blood:	n/a	chr3:119217571-119217579 chr3:119216827-119216835
37	POLR2A	chr3:119215964-119218008	SK-N-SH	brain:	n/a	n/a
38	POLR2A	chr3:119216640-119217948	MCF-7	breast:	n/a	n/a
39	POLR2A	chr3:119216051-119218651	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:119216582-119217009	GM12892	blood:	n/a	n/a
41	POLR2A	chr3:119216376-119217918	U87	brain:	n/a	n/a
42	MYC	chr3:119216700-119217817	K562	blood:	n/a	n/a
43	POLR2A	chr3:119216598-119216786	GM12878	blood:	n/a	n/a
44	GABPA	chr3:119216674-119217907	A549	lung:	n/a	chr3:119217351-119217360
45	POLR2A	chr3:119216294-119217975	Hela-S3	cervix:	n/a	n/a
46	GTF2F1	chr3:119216680-119217901	Hela-S3	cervix:	n/a	n/a
47	GABPA	chr3:119216471-119218033	A549	lung:	n/a	chr3:119217351-119217360
48	MYC	chr3:119216671-119217855	NB4	blood:	n/a	n/a
49	TCF12	chr3:119216607-119218013	A549	lung:	n/a	n/a
50	POLR2A	chr3:119216580-119217923	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
2	chr3:118954843..118957176-chr3:119215915..119217953,2	MCF-7	breast:
3	chr3:119216549..119217049-chr8:28243322..28244097,2	Hela-S3	cervix:
4	chr3:119201366..119207142-chr3:119210949..119217240,7	K562	blood:
5	chr3:119185641..119191138-chr3:119214841..119219392,9	MCF-7	breast:
6	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
7	chr3:119181428..119184178-chr3:119215849..119218868,6	K562	blood:
8	chr3:119186169..119189555-chr3:119214375..119219589,12	K562	blood:
9	chr3:119215767..119217677-chr3:119394561..119396315,2	MCF-7	breast:
10	chr3:119215976..119218932-chr3:119393949..119396539,3	K562	blood:
11	chr3:119186243..119189555-chr3:119215703..119218960,7	K562	blood:
12	chr3:119185037..119191105-chr3:119214944..119221331,23	MCF-7	breast:
13	chr3:119215904..119218714-chr3:135913674..135916504,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD80-3	chr3:119216525-119217028	ENSG00000272662.1

Variant related genes	Relation type
TIMMDC1	TF binding region
ENSG00000174579	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000186918	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11539377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11915398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916272	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11916344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11916488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917446	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11917642	0.85[EUR][1000 genomes]
rs11918271	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11919404	0.85[EUR][1000 genomes]
rs11919541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919760	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11921098	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11922005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923882	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11925305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16829840	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16829878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732414	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs503083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55696355	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55853418	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55968892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149432	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56195264	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56413426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56710033	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57168946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57389809	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57935532	0.95[EUR][1000 genomes]
rs58398719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639515	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58843212	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58978800	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59482964	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60006470	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6762095	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6763716	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764495	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6776387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779137	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs6783100	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6802790	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6808654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6810215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716649	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs72952928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72952950	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72970333	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72970352	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73857028	0.89[EUR][1000 genomes]
rs7621149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650975	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653469	0.85[GIH][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 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	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:119196800-119216800	Weak transcription	Small Intestine	intestine
3	chr3:119205800-119217000	Weak transcription	Spleen	Spleen
4	chr3:119207000-119216800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:119216000-119216800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:119216000-119216800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:119216000-119216800	Flanking Active TSS	Fetal Heart	heart
8	chr3:119216000-119216800	Flanking Active TSS	Dnd41	blood
9	chr3:119216000-119217000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:119216000-119218800	Active TSS	NHLF	lung
11	chr3:119216200-119216800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:119216200-119216800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr3:119216200-119216800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr3:119216200-119216800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr3:119216200-119216800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:119216200-119216800	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr3:119216200-119216800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
18	chr3:119216200-119216800	Flanking Active TSS	Hela-S3	cervix
19	chr3:119216200-119216800	Flanking Active TSS	HUVEC	blood vessel
20	chr3:119216200-119216800	Flanking Active TSS	Osteobl	bone
21	chr3:119216200-119217000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:119216200-119217000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:119216200-119217400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:119216200-119218200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:119216200-119218400	Active TSS	Brain Angular Gyrus	brain
26	chr3:119216200-119218600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr3:119216200-119218800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:119216200-119219200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr3:119216200-119219600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr3:119216200-119219600	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:119216200-119219800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:119216200-119220000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:119216400-119216800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:119216400-119216800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:119216400-119216800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:119216400-119216800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr3:119216400-119216800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr3:119216400-119216800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr3:119216400-119216800	Flanking Active TSS	Liver	Liver
40	chr3:119216400-119216800	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr3:119216400-119216800	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr3:119216400-119216800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr3:119216400-119216800	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr3:119216400-119216800	Flanking Active TSS	Fetal Kidney	kidney
45	chr3:119216400-119216800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:119216400-119217000	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr3:119216400-119217200	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr3:119216400-119217200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:119216400-119217400	Active TSS	Brain Germinal Matrix	brain
50	chr3:119216400-119218000	Active TSS	Fetal Brain Male	brain

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