Variant report

Variant	rs852538
Chromosome Location	chr7:5593624-5593625
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5593112..5594944-chr7:5719558..5721902,2	MCF-7	breast:
2	chr7:5456513..5458866-chr7:5593273..5595987,2	MCF-7	breast:
3	chr7:5581518..5584209-chr7:5593146..5596180,3	MCF-7	breast:
4	chr7:5558806..5574463-chr7:5583405..5604290,160	MCF-7	breast:
5	chr7:5320876..5323087-chr7:5592627..5594710,2	K562	blood:
6	chr7:5458987..5464555-chr7:5593156..5597256,5	K562	blood:
7	chr7:5462448..5464237-chr7:5593422..5596155,2	MCF-7	breast:
8	chr7:5464575..5468127-chr7:5593379..5596799,6	K562	blood:

Variant related genes	Relation type
ENSG00000182095	Chromatin interaction
ENSG00000164638	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000237738	Chromatin interaction
ENSG00000188365	Chromatin interaction
ENSG00000272953	Chromatin interaction
ENSG00000263900	Chromatin interaction
ENSG00000241269	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2908421	0.85[ASN][1000 genomes]
rs852492	0.83[ASN][1000 genomes]
rs852496	0.80[ASN][1000 genomes]
rs852501	0.85[ASN][1000 genomes]
rs852503	0.85[ASN][1000 genomes]
rs852504	0.85[ASN][1000 genomes]
rs852509	0.85[ASN][1000 genomes]
rs852513	0.81[ASN][1000 genomes]
rs852528	0.85[ASN][1000 genomes]
rs852534	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852535	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852537	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852539	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852540	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs852541	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer 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 miRNA target site	333 gene(s)	inside rSNPs	diseases
5	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
6	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
7	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
8	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
9	nsv887407	chr7:5432672-5605130	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	302 gene(s)	inside rSNPs	diseases
10	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
11	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
13	nsv887413	chr7:5521468-5607884	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	279 gene(s)	inside rSNPs	diseases
14	nsv1025434	chr7:5537571-5705283	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
15	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
16	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
17	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
18	nsv887414	chr7:5584934-5667645	Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
19	nsv887415	chr7:5584934-5675305	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
20	nsv887416	chr7:5584934-5695259	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5572600-5594600	Weak transcription	Right Atrium	heart
2	chr7:5587000-5594200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:5588800-5595000	Enhancers	Placenta	Placenta
4	chr7:5589000-5594400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:5589400-5594000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr7:5589400-5594200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:5589400-5594200	Weak transcription	Primary B cells from cord blood	blood
8	chr7:5589400-5594200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr7:5589400-5594200	Weak transcription	Spleen	Spleen
10	chr7:5589400-5594400	Weak transcription	HUVEC	blood vessel
11	chr7:5589400-5595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:5589400-5595200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:5589600-5594000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:5589600-5594200	Weak transcription	Esophagus	oesophagus
15	chr7:5589600-5594200	Weak transcription	Lung	lung
16	chr7:5589600-5594400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:5589600-5594400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:5589600-5594400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr7:5589600-5594400	Weak transcription	NHDF-Ad	bronchial
20	chr7:5589600-5594600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:5589600-5594800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:5589600-5595000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:5589600-5595000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr7:5589600-5595200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:5589800-5594400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr7:5590000-5594000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr7:5590000-5594200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:5590200-5594200	Weak transcription	NH-A	brain
29	chr7:5590400-5594200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr7:5590600-5594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:5590600-5594400	Weak transcription	Gastric	stomach
32	chr7:5590800-5594000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:5590800-5594200	Weak transcription	Ovary	ovary
34	chr7:5591600-5595000	Enhancers	Fetal Intestine Large	intestine
35	chr7:5591800-5594400	Enhancers	Colonic Mucosa	Colon
36	chr7:5591800-5595000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:5592000-5594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:5592400-5594200	Enhancers	A549	lung
39	chr7:5592400-5594400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:5592400-5594600	Flanking Active TSS	Hela-S3	cervix
41	chr7:5592400-5595000	Enhancers	Liver	Liver
42	chr7:5592600-5594200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr7:5592600-5594800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr7:5592600-5595000	Enhancers	Stomach Mucosa	stomach
45	chr7:5592800-5593800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr7:5592800-5594400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:5592800-5594600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:5593000-5594000	Enhancers	Fetal Heart	heart
49	chr7:5593000-5594000	Genic enhancers	Fetal Intestine Small	intestine
50	chr7:5593000-5594200	Enhancers	K562	blood

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