Variant report

Variant	rs10457702
Chromosome Location	chr6:140395530-140395531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:140390402..140393143-chr6:140395064..140396701,2	MCF-7	breast:
2	chr6:139693848..139696571-chr6:140395174..140397116,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10457036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457701	0.93[ASN][1000 genomes]
rs10484713	0.85[AFR][1000 genomes]
rs11155092	0.83[ASN][1000 genomes]
rs11155093	0.83[ASN][1000 genomes]
rs11155094	0.83[ASN][1000 genomes]
rs11155102	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11754775	0.83[ASN][1000 genomes]
rs12193363	0.83[ASN][1000 genomes]
rs12193742	0.83[ASN][1000 genomes]
rs12194624	0.83[ASN][1000 genomes]
rs12194665	0.83[ASN][1000 genomes]
rs12198042	0.83[ASN][1000 genomes]
rs12198595	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12198639	0.83[ASN][1000 genomes]
rs12198642	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12202850	0.93[ASN][1000 genomes]
rs12204229	0.83[ASN][1000 genomes]
rs12204306	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12205335	0.93[ASN][1000 genomes]
rs12207470	0.83[ASN][1000 genomes]
rs12210493	0.93[ASN][1000 genomes]
rs12212163	0.80[AMR][1000 genomes]
rs12212554	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12214000	0.83[ASN][1000 genomes]
rs12214369	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs12214414	0.83[ASN][1000 genomes]
rs12215417	0.83[ASN][1000 genomes]
rs12216315	0.83[ASN][1000 genomes]
rs169291	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs201284	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs201285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2024678	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2064502	0.83[ASN][1000 genomes]
rs34059065	0.93[ASN][1000 genomes]
rs72986764	0.83[ASN][1000 genomes]
rs72986775	0.93[ASN][1000 genomes]
rs9376479	0.83[ASN][1000 genomes]
rs9484322	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9495596	0.81[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10457702	IL22RA2	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140393000-140399200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:140393000-140399200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:140393000-140399200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:140393000-140399400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:140393000-140400000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:140393000-140400400	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:140393000-140400600	Weak transcription	Ovary	ovary
8	chr6:140393600-140396200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:140393600-140398800	Weak transcription	Fetal Heart	heart
10	chr6:140393600-140400400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:140393800-140399000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:140393800-140399000	Weak transcription	NH-A	brain
13	chr6:140393800-140399200	Weak transcription	Fetal Kidney	kidney
14	chr6:140394000-140398800	Weak transcription	HUVEC	blood vessel
15	chr6:140394000-140400000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:140394200-140396800	Weak transcription	Fetal Brain Female	brain
17	chr6:140394400-140399200	Weak transcription	Adipose Nuclei	Adipose
18	chr6:140394400-140403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:140394800-140398400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:140394800-140398800	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:140395000-140398800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:140395000-140398800	Weak transcription	Osteobl	bone
23	chr6:140395000-140399000	Weak transcription	Fetal Lung	lung
24	chr6:140395000-140399200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:140395000-140399400	Weak transcription	Fetal Brain Male	brain
26	chr6:140395000-140400000	Weak transcription	Hela-S3	cervix
27	chr6:140395200-140399000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:140395200-140399000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:140395200-140399400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:140395400-140397000	Weak transcription	NHDF-Ad	bronchial
31	chr6:140395400-140398400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:140395400-140398400	Weak transcription	NHLF	lung
33	chr6:140395400-140399200	Weak transcription	Fetal Stomach	stomach

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