Variant report

Variant	rs1800785
Chromosome Location	chr6:12289193-12289194
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	POLR2A	chr6:12287188-12308425	A549	lung:	n/a	n/a
2	ESR1	chr6:12289148-12289519	T-47D	breast:	n/a	n/a
3	MYC	chr6:12289151-12289345	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr6:12287484-12291106	A549	lung:	n/a	chr6:12290660-12290669
5	TCF12	chr6:12287489-12291132	A549	lung:	n/a	chr6:12288136-12288143
6	POLR2A	chr6:12289160-12299673	HUVEC	blood vessel:	n/a	n/a
7	REST	chr6:12288633-12289400	A549	lung:	n/a	n/a
8	GATA3	chr6:12286496-12291050	T-47D	breast:	n/a	chr6:12290453-12290463 chr6:12290456-12290465 chr6:12290036-12290046 chr6:12290456-12290463 chr6:12290457-12290474 chr6:12288770-12288779 chr6:12290455-12290465
9	JUND	chr6:12287854-12289429	T-47D	breast:	n/a	chr6:12288207-12288215 chr6:12289329-12289338
10	GATA3	chr6:12287755-12291217	A549	lung:	n/a	chr6:12290453-12290463 chr6:12290456-12290465 chr6:12290036-12290046 chr6:12290456-12290463 chr6:12290457-12290474 chr6:12288770-12288779 chr6:12290455-12290465
11	FOXA1	chr6:12289147-12289598	T-47D	breast:	n/a	n/a
12	POLR2A	chr6:12289054-12303672	HUVEC	blood vessel:	n/a	n/a
13	EP300	chr6:12289132-12291847	T-47D	breast:	n/a	chr6:12289410-12289420 chr6:12291576-12291590
14	POLR2A	chr6:12289050-12299813	HUVEC	blood vessel:	n/a	n/a
15	FOXA1	chr6:12289165-12289510	T-47D	breast:	n/a	n/a
16	JUND	chr6:12286241-12299466	T-47D	breast:	n/a	chr6:12291452-12291461 chr6:12293760-12293771 chr6:12291455-12291464 chr6:12290484-12290494 chr6:12295803-12295813 chr6:12291453-12291462 chr6:12293765-12293772 chr6:12290436-12290445 chr6:12293763-12293772 chr6:12295803-12295813 chr6:12286976-12286988 chr6:12293762-12293773 chr6:12291456-12291465 chr6:12288207-12288215 chr6:12289329-12289338 chr6:12291451-12291460
17	CTCF	chr6:12289183-12291188	A549	lung:	n/a	chr6:12289747-12289757 chr6:12290034-12290047 chr6:12289744-12289762 chr6:12289745-12289761
18	GATA3	chr6:12289164-12290884	T-47D	breast:	n/a	chr6:12290453-12290463 chr6:12290456-12290465 chr6:12290036-12290046 chr6:12290456-12290463 chr6:12290457-12290474 chr6:12290455-12290465
19	POLR2A	chr6:12288883-12289354	MCF10A-Er-Src	breast:	n/a	n/a
20	BCL3	chr6:12289038-12289934	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:11586656..11588418-chr6:12286272..12289815,3	MCF-7	breast:
2	chr6:12272974..12275123-chr6:12287770..12290178,2	K562	blood:
3	chr6:12286921..12289909-chr6:12330691..12332397,2	MCF-7	breast:
4	chr6:12009262..12013340-chr6:12286174..12290698,6	MCF-7	breast:
5	chr6:12158453..12160780-chr6:12288410..12290344,2	MCF-7	breast:
6	chr6:11585833..11588310-chr6:12287891..12289601,2	MCF-7	breast:
7	chr6:12009898..12015137-chr6:12286715..12292291,9	MCF-7	breast:
8	chr6:12286386..12290571-chr6:12602868..12606130,3	MCF-7	breast:
9	chr6:12286274..12290239-chr6:12290257..12295388,6	MCF-7	breast:
10	chr6:12281670..12285123-chr6:12286471..12289771,7	MCF-7	breast:
11	chr6:12286781..12289686-chr6:12349157..12350729,2	MCF-7	breast:
12	chr6:12243357..12246177-chr6:12286861..12290505,3	MCF-7	breast:
13	chr6:12272871..12275982-chr6:12286766..12289514,3	MCF-7	breast:
14	chr6:11667913..11670500-chr6:12287314..12290227,2	MCF-7	breast:
15	chr6:12288090..12290509-chr6:12483279..12484840,2	MCF-7	breast:
16	chr6:11655473..11656473-chr6:12288961..12290227,7	K562	blood:

Variant related genes	Relation type
EDN1	TF binding region
ENSG00000095951	Chromatin interaction
ENSG00000078401	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10478723	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800542	1.00[ASN][1000 genomes]
rs6458196	1.00[ASN][1000 genomes]
rs72830012	0.96[EUR][1000 genomes]
rs72830013	0.96[EUR][1000 genomes]
rs72830014	0.96[EUR][1000 genomes]
rs72830018	0.96[EUR][1000 genomes]
rs7750360	1.00[ASN][1000 genomes]
rs9296343	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462653	1.00[ASN][1000 genomes]
rs9462666	1.00[ASN][1000 genomes]
rs9471434	1.00[ASN][1000 genomes]
rs9471476	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830586	chr6:12130076-12295334	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12275400-12289400	Weak transcription	HSMMtube	muscle
2	chr6:12280000-12289600	Weak transcription	Adipose Nuclei	Adipose
3	chr6:12281400-12289400	Weak transcription	HSMM	muscle
4	chr6:12284200-12289800	Weak transcription	Aorta	Aorta
5	chr6:12285800-12289600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:12286200-12289800	Enhancers	Fetal Intestine Large	intestine
7	chr6:12287000-12289200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:12287000-12289600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:12287000-12291600	Active TSS	A549	lung
10	chr6:12287200-12289400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr6:12287200-12289600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr6:12287200-12289600	Weak transcription	NHDF-Ad	bronchial
13	chr6:12287200-12289800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:12287200-12289800	Enhancers	Placenta	Placenta
15	chr6:12287400-12289400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:12287400-12289400	Weak transcription	Osteobl	bone
17	chr6:12287400-12289600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:12287400-12289600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:12287600-12289200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:12287600-12289400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr6:12287600-12289800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:12287600-12289800	Enhancers	Colonic Mucosa	Colon
23	chr6:12287800-12289400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:12287800-12289400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:12287800-12289400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr6:12287800-12289600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr6:12288000-12289200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:12288000-12289200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:12288000-12289200	Enhancers	GM12878-XiMat	blood
30	chr6:12288000-12289400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:12288200-12289600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr6:12288200-12289800	Weak transcription	Stomach Mucosa	stomach
33	chr6:12288200-12290000	Flanking Active TSS	HMEC	breast
34	chr6:12288400-12289400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:12288400-12289400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:12288400-12289600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:12288400-12289600	Flanking Active TSS	NHEK	skin
38	chr6:12288600-12289400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr6:12288600-12289600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr6:12288800-12289200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:12288800-12289200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr6:12288800-12289800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:12288800-12290000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:12288800-12291800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:12289000-12289200	Enhancers	Fetal Intestine Small	intestine
46	chr6:12289000-12289400	Enhancers	Hela-S3	cervix
47	chr6:12289000-12289600	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr6:12289000-12289800	Weak transcription	Esophagus	oesophagus
49	chr6:12289000-12289800	Weak transcription	Pancreas	Pancrea
50	chr6:12289000-12289800	Flanking Active TSS	HUVEC	blood vessel

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