Variant report

Variant	rs2636961
Chromosome Location	chr5:118862971-118862972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs2257900	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2257901	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2459726	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs246965	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs246966	0.81[MKK][hapmap]
rs246967	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2546210	1.00[CEU][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs257970	0.96[CEU][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs257976	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26181	0.95[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26184	0.96[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2636962	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636964	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2636968	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2678070	0.91[CHD][hapmap]
rs2678074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2678076	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2678091	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs27938	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs32664	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs382719	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3850202	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs389760	0.85[ASN][1000 genomes]
rs39970	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs422297	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs426899	0.84[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs439954	1.00[JPT][hapmap]
rs442919	0.87[ASN][1000 genomes]
rs442923	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs450118	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs460274	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs463098	0.96[CEU][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs467076	0.83[CHD][hapmap];1.00[JPT][hapmap]

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	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1016271	chr5:118836891-119487982	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv882776	chr5:118859546-118915408	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2636961	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:118832400-118878200	Weak transcription	NH-A	brain
3	chr5:118832600-118868600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:118838000-118869200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:118840200-118878400	Weak transcription	Psoas Muscle	Psoas
6	chr5:118841000-118880000	Weak transcription	Brain Germinal Matrix	brain
7	chr5:118841200-118880000	Weak transcription	A549	lung
8	chr5:118841400-118873200	Weak transcription	Fetal Brain Male	brain
9	chr5:118845800-118868800	Weak transcription	Fetal Heart	heart
10	chr5:118846800-118878200	Weak transcription	NHLF	lung
11	chr5:118847000-118863000	Weak transcription	NHDF-Ad	bronchial
12	chr5:118847000-118868000	Weak transcription	K562	blood
13	chr5:118847200-118873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:118847200-118877800	Weak transcription	Small Intestine	intestine
15	chr5:118847200-118878200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:118847200-118879800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:118847400-118863000	Weak transcription	HMEC	breast
18	chr5:118847400-118872000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:118847400-118873000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:118847400-118873200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr5:118847400-118873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr5:118847400-118875800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr5:118847400-118876000	Weak transcription	Colonic Mucosa	Colon
24	chr5:118847400-118878200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr5:118847400-118879800	Weak transcription	HSMMtube	muscle
26	chr5:118847600-118863400	Weak transcription	Brain Angular Gyrus	brain
27	chr5:118847600-118865000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:118847600-118873200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:118847600-118873400	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:118847600-118873600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:118847600-118877600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:118847600-118878200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:118847600-118879800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:118848000-118863400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr5:118848200-118863200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:118848600-118863800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:118850000-118865600	Weak transcription	GM12878-XiMat	blood
38	chr5:118851800-118876400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:118852000-118863400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr5:118852400-118863200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:118852800-118878200	Weak transcription	Aorta	Aorta
42	chr5:118853000-118880200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:118853400-118863400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:118853400-118878200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:118853400-118878200	Weak transcription	Esophagus	oesophagus
46	chr5:118853400-118878200	Weak transcription	Gastric	stomach
47	chr5:118854200-118875600	Weak transcription	Pancreas	Pancrea
48	chr5:118854400-118877600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:118854400-118878400	Weak transcription	Spleen	Spleen
50	chr5:118854400-118879600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links