Variant report

Variant	rs6531997
Chromosome Location	chr4:88365487-88365488
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88361602..88363140-chr4:88363791..88366603,2	MCF-7	breast:
2	chr4:88342378..88346157-chr4:88365314..88366974,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170502	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10008963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10009776	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10015443	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10017282	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10034240	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10213468	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11097151	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13119798	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13122902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28439403	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4388049	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4693163	0.81[JPT][hapmap]
rs6531987	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6531988	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6531994	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6531995	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67796586	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6816136	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6847168	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7666886	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7673045	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7695235	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9307036	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9968511	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
2	nsv1011882	chr4:88363959-88402477	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88344400-88398600	Weak transcription	Gastric	stomach
2	chr4:88345200-88400000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:88345200-88416400	Weak transcription	Colonic Mucosa	Colon
4	chr4:88345400-88372400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:88345400-88378800	Weak transcription	A549	lung
6	chr4:88345800-88372200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:88346200-88370600	Weak transcription	Thymus	Thymus
8	chr4:88346200-88382600	Weak transcription	NHLF	lung
9	chr4:88346400-88366200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:88346400-88369600	Weak transcription	Right Atrium	heart
11	chr4:88346400-88372200	Weak transcription	Aorta	Aorta
12	chr4:88346400-88379400	Weak transcription	Small Intestine	intestine
13	chr4:88346600-88371600	Weak transcription	Spleen	Spleen
14	chr4:88346600-88372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:88346600-88410400	Weak transcription	Esophagus	oesophagus
16	chr4:88346800-88371400	Weak transcription	Lung	lung
17	chr4:88347200-88366000	Weak transcription	NH-A	brain
18	chr4:88347200-88372000	Weak transcription	NHEK	skin
19	chr4:88349000-88372400	Weak transcription	HSMMtube	muscle
20	chr4:88349000-88375400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:88349400-88381800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr4:88350600-88380600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:88351200-88379000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:88351400-88382400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:88351600-88414600	Weak transcription	Psoas Muscle	Psoas
26	chr4:88351800-88366600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:88352600-88387200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:88353400-88377000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:88354800-88381600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:88356000-88377600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:88356200-88367400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:88356200-88367600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:88356200-88368000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:88356400-88376400	Strong transcription	Liver	Liver
35	chr4:88356400-88377200	Weak transcription	Fetal Brain Male	brain
36	chr4:88356600-88382000	Weak transcription	Brain Germinal Matrix	brain
37	chr4:88357000-88366800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:88357000-88367400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr4:88357200-88366800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:88357400-88367200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:88357600-88372000	Weak transcription	Hela-S3	cervix
42	chr4:88357600-88380000	Weak transcription	Brain Angular Gyrus	brain
43	chr4:88357800-88367000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:88357800-88381600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr4:88358000-88365600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:88358400-88370600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:88359200-88367400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:88359400-88368200	Strong transcription	Fetal Thymus	thymus
49	chr4:88359800-88382200	Weak transcription	Fetal Brain Female	brain
50	chr4:88360400-88381800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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