Variant report

Variant	rs7630858
Chromosome Location	chr3:24429213-24429214
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	chr3:24395912..24398786-chr3:24427105..24429295,2	K562	blood:
2	chr3:24428751..24431920-chr3:24433157..24435631,4	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11129150	0.89[EUR][1000 genomes]
rs11129152	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918018	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12495379	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13065876	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13086388	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1505286	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1505287	0.80[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1505289	0.80[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs17014597	0.85[ASN][1000 genomes]
rs17014605	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135147	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2217883	0.96[CEU][hapmap]
rs28380451	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35340172	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4276128	0.89[EUR][1000 genomes]
rs4300958	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4309672	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4423711	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4491844	0.87[ASN][1000 genomes]
rs4541352	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4602332	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4630886	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4858608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858610	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4858613	0.96[CEU][hapmap]
rs6550865	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6769978	0.99[ASN][1000 genomes]
rs6771995	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6786474	0.93[ASN][1000 genomes]
rs7611219	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7648757	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9310739	0.88[EUR][1000 genomes]
rs9310740	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9816509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826887	0.88[EUR][1000 genomes]
rs9839986	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs9851523	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs9852824	0.88[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][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	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7630858	NKIRAS1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24394000-24431400	Weak transcription	Gastric	stomach
2	chr3:24418000-24429800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:24418000-24430000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:24418200-24429800	Weak transcription	Fetal Lung	lung
5	chr3:24420200-24441600	Weak transcription	Liver	Liver
6	chr3:24421200-24429800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:24422000-24430000	Weak transcription	K562	blood
8	chr3:24427000-24432400	Weak transcription	Lung	lung
9	chr3:24427000-24433000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:24427600-24431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:24427800-24432000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:24428000-24429400	Enhancers	HSMM	muscle
13	chr3:24428000-24431600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr3:24428000-24432200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:24428000-24432200	Enhancers	HMEC	breast
16	chr3:24428200-24431800	Enhancers	NHEK	skin
17	chr3:24428400-24429600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:24428400-24430000	Enhancers	NHDF-Ad	bronchial
19	chr3:24428400-24430200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:24428600-24429600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:24428600-24430400	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:24428600-24431600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:24428600-24431800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr3:24428600-24432000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:24428600-24432800	Enhancers	Colon Smooth Muscle	Colon
26	chr3:24428800-24429800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:24428800-24429800	Enhancers	Fetal Muscle Leg	muscle
28	chr3:24428800-24432400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:24428800-24432800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:24429000-24429600	Enhancers	Aorta	Aorta
31	chr3:24429000-24429800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:24429000-24430800	Enhancers	Psoas Muscle	Psoas
33	chr3:24429000-24431800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:24429000-24432600	Enhancers	HSMMtube	muscle
35	chr3:24429000-24432800	Enhancers	Adipose Nuclei	Adipose
36	chr3:24429000-24432800	Enhancers	Pancreas	Pancrea
37	chr3:24429200-24429800	Weak transcription	Fetal Intestine Small	intestine
38	chr3:24429200-24429800	Enhancers	Right Atrium	heart
39	chr3:24429200-24430400	Enhancers	Fetal Kidney	kidney
40	chr3:24429200-24430600	Enhancers	Right Ventricle	heart
41	chr3:24429200-24430800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:24429200-24432600	Enhancers	Stomach Smooth Muscle	stomach
43	chr3:24429200-24432800	Enhancers	Fetal Intestine Large	intestine
44	chr3:24429200-24432800	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links