Variant report

Variant	rs6975496
Chromosome Location	chr7:12689458-12689459
allele	A/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	GATA3	chr7:12689033-12689598	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:12688194..12690298-chr7:12711054..12712934,2	MCF-7	breast:
2	chr7:12688601..12690715-chr7:12695184..12696876,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229233	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1024581	1.00[EUR][1000 genomes]
rs10271745	0.91[AMR][1000 genomes]
rs11983218	1.00[EUR][1000 genomes]
rs17166200	1.00[EUR][1000 genomes]
rs17166232	1.00[EUR][1000 genomes]
rs73294923	1.00[EUR][1000 genomes]
rs73294941	1.00[EUR][1000 genomes]
rs7782523	1.00[EUR][1000 genomes]
rs7796394	1.00[EUR][1000 genomes]
rs7808884	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv1021371	chr7:12530491-12710429	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1030764	chr7:12532287-12710429	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv830907	chr7:12661239-12818250	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv1019962	chr7:12683139-12699056	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12663800-12693000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:12664800-12700200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:12675800-12699800	Weak transcription	Esophagus	oesophagus
4	chr7:12679000-12693800	Weak transcription	Colonic Mucosa	Colon
5	chr7:12681400-12690800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:12682400-12693400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:12683600-12690400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:12683600-12693000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr7:12685800-12692800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:12686800-12689600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:12686800-12689800	Enhancers	NHEK	skin
12	chr7:12687000-12689600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:12687800-12690200	Enhancers	A549	lung
14	chr7:12687800-12692000	Weak transcription	Stomach Mucosa	stomach
15	chr7:12687800-12692600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr7:12687800-12693000	Weak transcription	NH-A	brain
17	chr7:12687800-12693000	Weak transcription	Osteobl	bone
18	chr7:12688000-12696200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:12688200-12689600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr7:12688200-12689600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:12688400-12693200	Weak transcription	K562	blood
22	chr7:12688600-12691200	Weak transcription	Hela-S3	cervix
23	chr7:12688800-12692400	Weak transcription	Placenta	Placenta
24	chr7:12688800-12693000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr7:12689000-12692200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links