Variant report

Variant	rs3822423
Chromosome Location	chr5:43388399-43388400
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43311092..43314339-chr5:43385527..43389897,4	MCF-7	breast:
2	chr5:43066485..43068592-chr5:43387245..43389179,2	MCF-7	breast:
3	chr5:43119482..43123443-chr5:43388047..43390773,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000112972	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10043868	1.00[ASN][1000 genomes]
rs10044795	0.94[ASN][1000 genomes]
rs10044799	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055041	0.81[ASN][1000 genomes]
rs10062256	1.00[ASN][1000 genomes]
rs1025299	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461740	1.00[JPT][hapmap]
rs10473309	0.97[ASN][1000 genomes]
rs1083833	0.94[ASN][1000 genomes]
rs10941642	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12656650	1.00[JPT][hapmap]
rs12657635	1.00[JPT][hapmap]
rs12657724	1.00[JPT][hapmap]
rs12659627	1.00[JPT][hapmap]
rs13155888	1.00[JPT][hapmap]
rs13160431	1.00[JPT][hapmap]
rs13164705	1.00[ASN][1000 genomes]
rs13165869	1.00[JPT][hapmap]
rs13168053	1.00[JPT][hapmap]
rs13169908	0.85[CHB][hapmap]
rs13173517	1.00[JPT][hapmap]
rs13186439	0.85[CHB][hapmap]
rs16873319	1.00[JPT][hapmap]
rs2042950	1.00[JPT][hapmap]
rs28461402	1.00[ASN][1000 genomes]
rs34060183	1.00[ASN][1000 genomes]
rs34880892	0.97[ASN][1000 genomes]
rs35001439	0.97[ASN][1000 genomes]
rs35446538	0.97[ASN][1000 genomes]
rs36000604	0.91[ASN][1000 genomes]
rs36025143	1.00[ASN][1000 genomes]
rs36062172	0.91[ASN][1000 genomes]
rs36063200	1.00[ASN][1000 genomes]
rs3733767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756417	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3797152	1.00[ASN][1000 genomes]
rs3797153	1.00[ASN][1000 genomes]
rs3806871	1.00[CHD][hapmap]
rs4264950	1.00[JPT][hapmap]
rs4438885	1.00[JPT][hapmap]
rs4498257	1.00[JPT][hapmap]
rs4533897	1.00[JPT][hapmap]
rs6451687	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6451688	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861429	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865915	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6866007	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868939	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6878207	0.91[ASN][1000 genomes]
rs6889653	1.00[JPT][hapmap]
rs6890108	1.00[JPT][hapmap]
rs6892337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs71590642	1.00[ASN][1000 genomes]
rs71610306	0.97[ASN][1000 genomes]
rs71629107	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720858	1.00[JPT][hapmap]
rs9292877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43368600-43389800	Weak transcription	Stomach Mucosa	stomach
2	chr5:43368800-43396400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr5:43370000-43396200	Weak transcription	Primary B cells from cord blood	blood
4	chr5:43371800-43396800	Weak transcription	Small Intestine	intestine
5	chr5:43372200-43396800	Weak transcription	Gastric	stomach
6	chr5:43373200-43396400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr5:43374600-43396400	Weak transcription	Adipose Nuclei	Adipose
8	chr5:43375000-43396800	Weak transcription	Spleen	Spleen
9	chr5:43376200-43389800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr5:43377200-43396800	Weak transcription	Colonic Mucosa	Colon
11	chr5:43378600-43396200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:43378800-43396400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr5:43379000-43396400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr5:43379200-43395800	Weak transcription	Placenta	Placenta
15	chr5:43379400-43388600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:43380400-43396400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:43382200-43396400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:43384800-43388800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:43385400-43388400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:43386000-43388600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr5:43386000-43388600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:43386000-43389000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr5:43386000-43396800	Weak transcription	Esophagus	oesophagus
24	chr5:43386200-43388600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:43386200-43389200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr5:43386400-43388400	Enhancers	GM12878-XiMat	blood
27	chr5:43386400-43388600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:43386400-43389000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:43386400-43389200	Strong transcription	Primary T cells from cord blood	blood
30	chr5:43386600-43389000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:43386800-43388600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr5:43387000-43388400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:43387000-43388600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr5:43387000-43389000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr5:43387200-43388600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr5:43387200-43388600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:43387400-43389200	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:43387600-43388600	Weak transcription	A549	lung
39	chr5:43387600-43396400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:43387800-43396200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:43388000-43396200	Weak transcription	Thymus	Thymus
42	chr5:43388000-43396400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:43388000-43396800	Weak transcription	Lung	lung

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