Variant report

Variant	rs13079094
Chromosome Location	chr3:119882088-119882089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119816323..119819155-chr3:119879849..119882520,2	MCF-7	breast:
2	chr3:119879846..119883232-chr3:119884933..119889018,3	K562	blood:
3	chr3:119880098..119883232-chr3:119884308..119887648,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1079784	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934510	0.81[EUR][1000 genomes]
rs10934520	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061630	1.00[JPT][hapmap]
rs13064815	0.85[AMR][1000 genomes]
rs13073885	0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs1492272	1.00[JPT][hapmap]
rs2029607	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34032950	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34537735	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34720062	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280462	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35791817	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902169	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35977875	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676703	0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4676811	1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs55871529	0.83[AMR][1000 genomes]
rs6438575	1.00[JPT][hapmap]
rs6776878	1.00[JPT][hapmap]
rs6792814	0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs7630226	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633395	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634938	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13079094	ARHGAP31	cis	parietal	SCAN
rs13079094	KPNA1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119877600-119882600	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:119879400-119882400	Enhancers	Hela-S3	cervix
4	chr3:119879400-119882600	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:119879400-119886000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:119879400-119886000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:119879600-119882600	Weak transcription	Adipose Nuclei	Adipose
8	chr3:119879600-119883000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:119880000-119888600	Weak transcription	A549	lung
10	chr3:119880400-119883400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:119881000-119883000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:119881000-119883200	Enhancers	Fetal Intestine Large	intestine
13	chr3:119881000-119883200	Enhancers	Fetal Intestine Small	intestine
14	chr3:119881200-119883000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:119881200-119883200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:119881400-119883600	Weak transcription	Placenta	Placenta
17	chr3:119881600-119882600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:119881600-119882800	Weak transcription	NHDF-Ad	bronchial
19	chr3:119881600-119886200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:119881600-119888000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:119881800-119886200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:119881800-119888000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:119881800-119888600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:119882000-119882200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:119882000-119882800	Flanking Active TSS	HepG2	liver

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