Variant report

Variant	rs6952330
Chromosome Location	chr7:101252365-101252366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101248988..101252731-chr7:101456839..101459495,3	MCF-7	breast:
2	chr7:101245631..101247804-chr7:101249820..101253085,4	MCF-7	breast:
3	chr7:101244039..101255564-chr7:101454524..101463981,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10230317	0.93[ASN][1000 genomes]
rs10253090	0.97[ASN][1000 genomes]
rs10260032	0.93[ASN][1000 genomes]
rs10263222	0.93[ASN][1000 genomes]
rs10267748	0.93[ASN][1000 genomes]
rs10275446	0.93[ASN][1000 genomes]
rs10275576	0.93[ASN][1000 genomes]
rs17135656	0.93[ASN][1000 genomes]
rs17135662	0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs1981582	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2158724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2410855	0.93[ASN][1000 genomes]
rs28526614	0.93[ASN][1000 genomes]
rs4727499	0.93[ASN][1000 genomes]
rs4729736	0.82[CHD][hapmap]
rs6945206	0.93[ASN][1000 genomes]
rs6945374	0.93[ASN][1000 genomes]
rs6965503	0.93[ASN][1000 genomes]
rs6979523	0.93[ASN][1000 genomes]
rs6979532	0.93[ASN][1000 genomes]
rs7793853	0.93[ASN][1000 genomes]
rs7794011	0.93[ASN][1000 genomes]
rs7803577	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv888821	chr7:101091470-101311540	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv831078	chr7:101094945-101257486	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv888822	chr7:101105017-101330734	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv888824	chr7:101109073-101330734	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv888825	chr7:101168283-101330734	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1018544	chr7:101225639-101424889	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539045	chr7:101225639-101424889	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv888826	chr7:101230768-101277334	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv482758	chr7:101231458-101395219	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6952330	AGFG2	cis	parietal	SCAN
rs6952330	MGC72080	cis	cerebellum	SCAN
rs6952330	MEPCE	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101251600-101252600	Enhancers	Gastric	stomach
2	chr7:101251600-101252600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr7:101251600-101252800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:101251600-101252800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:101251600-101252800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:101251600-101252800	Enhancers	Placenta	Placenta
7	chr7:101251600-101252800	Enhancers	Stomach Mucosa	stomach
8	chr7:101251600-101252800	Enhancers	HMEC	breast
9	chr7:101251800-101252600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr7:101251800-101252800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr7:101251800-101252800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:101251800-101252800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:101251800-101252800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:101251800-101252800	Enhancers	Pancreas	Pancrea
15	chr7:101251800-101252800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr7:101252000-101252400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:101252000-101252600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:101252000-101252600	Enhancers	Fetal Intestine Small	intestine
19	chr7:101252000-101252800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr7:101252000-101252800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
21	chr7:101252000-101252800	Enhancers	Duodenum Mucosa	Duodenum
22	chr7:101252000-101252800	Enhancers	Esophagus	oesophagus
23	chr7:101252000-101252800	Enhancers	Fetal Intestine Large	intestine
24	chr7:101252200-101252600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr7:101252200-101252800	Bivalent Enhancer	NHEK	skin

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