Variant report

Variant	rs4858608
Chromosome Location	chr3:24428821-24428822
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24395912..24398786-chr3:24427105..24429295,2	K562	blood:
2	chr3:24428751..24431920-chr3:24433157..24435631,4	K562	blood:
3	chr3:24426145..24428959-chr3:24533160..24535745,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228791	Chromatin interaction

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

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

rs_ID	r²[population]
rs11129150	0.93[EUR][1000 genomes]
rs11129152	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918018	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12495379	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13065876	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13086388	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1505286	0.87[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];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs17014597	0.85[ASN][1000 genomes]
rs17014605	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2135147	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2217883	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs28380451	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35340172	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4276128	0.93[EUR][1000 genomes]
rs4300958	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4309672	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[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	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4630886	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4858610	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4858613	0.89[CEU][hapmap];0.84[TSI][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	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6786474	0.93[ASN][1000 genomes]
rs7611219	0.83[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7630858	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648757	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9310739	0.92[EUR][1000 genomes]
rs9310740	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9816509	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826887	0.91[EUR][1000 genomes]
rs9839986	0.89[CEU][hapmap]
rs9851523	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs9852824	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[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
rs4858608	NKIRAS1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24394000-24431400	Weak transcription	Gastric	stomach
2	chr3:24418000-24429200	Weak transcription	Right Ventricle	heart
3	chr3:24418000-24429800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:24418000-24430000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:24418200-24429200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:24418200-24429800	Weak transcription	Fetal Lung	lung
7	chr3:24419000-24429000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:24419000-24429000	Weak transcription	Pancreas	Pancrea
9	chr3:24419000-24429200	Weak transcription	Left Ventricle	heart
10	chr3:24420200-24441600	Weak transcription	Liver	Liver
11	chr3:24421200-24429000	Weak transcription	Psoas Muscle	Psoas
12	chr3:24421200-24429800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:24422000-24430000	Weak transcription	K562	blood
14	chr3:24427000-24432400	Weak transcription	Lung	lung
15	chr3:24427000-24433000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:24427200-24429200	Weak transcription	Fetal Intestine Large	intestine
17	chr3:24427600-24431000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:24427800-24429200	Enhancers	Fetal Intestine Small	intestine
19	chr3:24427800-24432000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:24428000-24429000	Weak transcription	Aorta	Aorta
21	chr3:24428000-24429400	Enhancers	HSMM	muscle
22	chr3:24428000-24431600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr3:24428000-24432200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:24428000-24432200	Enhancers	HMEC	breast
25	chr3:24428200-24431800	Enhancers	NHEK	skin
26	chr3:24428400-24429600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:24428400-24430000	Enhancers	NHDF-Ad	bronchial
28	chr3:24428400-24430200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:24428600-24429000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:24428600-24429200	Enhancers	NHLF	lung
31	chr3:24428600-24429600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:24428600-24430400	Enhancers	Rectal Smooth Muscle	rectum
33	chr3:24428600-24431600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:24428600-24431800	Enhancers	Placenta Amnion	Placenta Amnion
35	chr3:24428600-24432000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:24428600-24432800	Enhancers	Colon Smooth Muscle	Colon
37	chr3:24428800-24429000	Flanking Active TSS	HSMMtube	muscle
38	chr3:24428800-24429800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:24428800-24429800	Enhancers	Fetal Muscle Leg	muscle
40	chr3:24428800-24432400	Weak transcription	Brain Angular Gyrus	brain
41	chr3:24428800-24432800	Enhancers	Skeletal Muscle Male	skeletal muscle

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