Variant report

Variant	rs13176923
Chromosome Location	chr5:61552759-61552760
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	chr5:61551611..61555704-chr5:61555776..61558862,4	K562	blood:
2	chr5:61550007..61554674-chr5:61558868..61565665,10	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1108158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740652	0.80[ASN][1000 genomes]
rs11742167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11750109	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12655562	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13155253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13156073	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs13156695	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13161789	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13162519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13162821	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13169321	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13170425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13174779	0.80[ASN][1000 genomes]
rs13178729	0.87[AMR][1000 genomes]
rs13181377	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13189446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs153860	0.92[CHB][hapmap]
rs153864	1.00[CHB][hapmap]
rs153866	0.92[CHB][hapmap]
rs153873	0.90[CHB][hapmap]
rs16875037	0.80[ASN][1000 genomes]
rs16890613	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16890618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16890628	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16890634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16890651	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16898838	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2059162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272291	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2441115	0.90[CHB][hapmap]
rs27090	0.90[CHB][hapmap]
rs34220654	0.80[ASN][1000 genomes]
rs34596001	0.80[ASN][1000 genomes]
rs35058	0.92[CHB][hapmap]
rs35238667	0.80[ASN][1000 genomes]
rs35311093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35572300	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35672643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35699711	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35744020	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35746052	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35794032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35808056	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35842742	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36105063	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776612	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3776614	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3822487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4289514	0.80[ASN][1000 genomes]
rs71617425	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71617426	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71617427	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71617428	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7446543	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs814169	1.00[CHB][hapmap]
rs971965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv830318	chr5:61415713-61623320	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv11317	chr5:61501951-61555756	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv821303	chr5:61501951-61555756	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv1826874	chr5:61512183-61552823	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2755585	chr5:61535831-61618595	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13176923	KIF2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61549800-61553800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr5:61551800-61553000	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr5:61552000-61552800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
4	chr5:61552000-61552800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
5	chr5:61552000-61552800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr5:61552000-61552800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr5:61552000-61552800	Enhancers	Adipose Nuclei	Adipose
8	chr5:61552000-61552800	Enhancers	Brain Hippocampus Middle	brain
9	chr5:61552000-61552800	Enhancers	Fetal Lung	lung
10	chr5:61552000-61552800	Enhancers	Fetal Thymus	thymus
11	chr5:61552000-61552800	Enhancers	Thymus	Thymus
12	chr5:61552000-61553000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr5:61552000-61553000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:61552000-61553000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:61552000-61553000	Enhancers	Fetal Kidney	kidney
16	chr5:61552000-61553000	Enhancers	Fetal Muscle Leg	muscle
17	chr5:61552000-61553200	Enhancers	Brain Germinal Matrix	brain
18	chr5:61552000-61553200	Enhancers	HUVEC	blood vessel
19	chr5:61552000-61553200	Enhancers	K562	blood
20	chr5:61552000-61553600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:61552200-61552800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:61552200-61552800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr5:61552200-61552800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:61552200-61552800	Enhancers	Brain Cingulate Gyrus	brain
25	chr5:61552200-61553000	Enhancers	Primary B cells from peripheral blood	blood
26	chr5:61552200-61553000	Enhancers	Primary hematopoietic stem cells	blood
27	chr5:61552200-61553000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr5:61552200-61553000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:61552200-61553000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr5:61552200-61553000	Enhancers	NHEK	skin
31	chr5:61552400-61552800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr5:61552400-61552800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:61552400-61552800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:61552400-61552800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:61552400-61552800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:61552400-61552800	Enhancers	HMEC	breast
37	chr5:61552400-61553000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:61552400-61553000	Flanking Active TSS	Dnd41	blood
39	chr5:61552400-61553000	Flanking Active TSS	GM12878-XiMat	blood
40	chr5:61552400-61555600	Weak transcription	Pancreas	Pancrea
41	chr5:61552600-61552800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:61552600-61552800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:61552600-61552800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr5:61552600-61552800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:61552600-61552800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:61552600-61552800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
47	chr5:61552600-61553000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:61552600-61553000	Enhancers	Brain Angular Gyrus	brain
49	chr5:61552600-61553200	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links