Variant report

Variant	rs10516522
Chromosome Location	chr4:106600838-106600839
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	chr4:106600442..106602529-chr4:106626797..106629772,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INTS12-2	chr4:106600207-106601251	NONHSAT097685

Variant related genes	Relation type
ENSG00000138785	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10019217	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10030620	0.80[ASN][1000 genomes]
rs10049527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11930244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11930965	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11936611	0.82[ASN][1000 genomes]
rs11942577	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[TSI][hapmap]
rs12504088	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12511885	0.90[GIH][hapmap];0.95[ASN][1000 genomes]
rs12512339	0.90[ASN][1000 genomes]
rs13110070	0.85[ASN][1000 genomes]
rs13145251	0.83[ASN][1000 genomes]
rs17036093	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17036097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17036102	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17036158	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17036254	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2193852	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2193853	0.92[ASN][1000 genomes]
rs2193854	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs28370551	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28391170	1.00[ASN][1000 genomes]
rs28450989	1.00[ASN][1000 genomes]
rs28559909	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28698939	0.85[ASN][1000 genomes]
rs3796926	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235415	0.87[ASN][1000 genomes]
rs4490460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698950	0.93[ASN][1000 genomes]
rs4698951	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4699192	0.85[ASN][1000 genomes]
rs4699193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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]
rs4699194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699195	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699198	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4699199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58388061	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58914657	0.83[ASN][1000 genomes]
rs59961848	0.84[ASN][1000 genomes]
rs60774107	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60861135	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6817029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6820671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6825379	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs6826631	0.82[ASN][1000 genomes]
rs6843771	0.82[ASN][1000 genomes]
rs7658055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7659526	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7665588	0.92[ASN][1000 genomes]
rs7696836	0.85[ASN][1000 genomes]
rs7697619	0.95[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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106559400-106602800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:106578600-106607000	Weak transcription	Small Intestine	intestine
3	chr4:106580400-106603400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:106580400-106613200	Weak transcription	Fetal Intestine Small	intestine
5	chr4:106587800-106629000	Weak transcription	Lung	lung
6	chr4:106593000-106603800	Weak transcription	Aorta	Aorta
7	chr4:106594000-106603400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:106595400-106603000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:106597000-106610000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:106597200-106603400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:106597400-106602800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:106598600-106613000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr4:106598800-106601600	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr4:106599000-106603600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:106599000-106614400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:106599200-106603200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:106599200-106613800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:106599400-106603200	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:106599600-106603000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:106599600-106603200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:106599800-106602600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:106599800-106603600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:106600200-106601000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr4:106600200-106601000	Enhancers	Liver	Liver
25	chr4:106600200-106601000	Enhancers	Osteobl	bone
26	chr4:106600200-106601200	Enhancers	Gastric	stomach
27	chr4:106600200-106601200	Enhancers	Pancreas	Pancrea
28	chr4:106600200-106601200	Enhancers	Psoas Muscle	Psoas
29	chr4:106600200-106602200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr4:106600400-106601200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr4:106600400-106601200	Enhancers	HSMM	muscle
32	chr4:106600400-106601400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:106600400-106602600	Weak transcription	Fetal Thymus	thymus
34	chr4:106600400-106628600	Weak transcription	Colonic Mucosa	Colon
35	chr4:106600600-106601200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:106600600-106601200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:106600600-106602600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:106600600-106602600	Weak transcription	Adipose Nuclei	Adipose
39	chr4:106600600-106603000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr4:106600600-106603400	Weak transcription	NHDF-Ad	bronchial
41	chr4:106600600-106603600	Weak transcription	NH-A	brain
42	chr4:106600600-106603800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:106600600-106603800	Weak transcription	Ovary	ovary
44	chr4:106600600-106628400	Weak transcription	Stomach Mucosa	stomach
45	chr4:106600800-106602400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr4:106600800-106602600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:106600800-106602600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:106600800-106602600	Weak transcription	Fetal Intestine Large	intestine
49	chr4:106600800-106603400	Weak transcription	HSMMtube	muscle
50	chr4:106600800-106603600	Weak transcription	HUVEC	blood vessel

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