Variant report

Variant	rs2856338
Chromosome Location	chr12:11904752-11904753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1009951	0.89[CEU][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs1009953	0.89[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1009954	0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs10845407	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10845408	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10845410	0.87[EUR][1000 genomes]
rs11054423	0.81[TSI][hapmap]
rs11615175	0.83[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap]
rs12228191	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12369491	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12828066	0.83[MEX][hapmap]
rs17818461	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs17818498	0.81[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs17818624	0.89[CHD][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2051525	0.85[JPT][hapmap]
rs2187641	0.92[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2416882	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2416883	0.96[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2724588	0.81[TSI][hapmap]
rs2724599	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724600	0.91[EUR][1000 genomes]
rs2724633	0.91[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2724635	0.84[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs2724645	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2856324	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs2856344	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2860431	0.92[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs2900208	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4763719	0.89[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4763720	0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4763721	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7488701	0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs762717	0.89[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs972798	0.92[CEU][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2856338	KLRA1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:11883800-11906000	Weak transcription	Liver	Liver
3	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
5	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:11894600-11905200	Weak transcription	Fetal Intestine Small	intestine
8	chr12:11894600-11905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:11894600-11905400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:11894600-11906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:11894600-11908400	Weak transcription	Psoas Muscle	Psoas
12	chr12:11894800-11906000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:11894800-11906600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:11895000-11906000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:11895000-11906800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:11895000-11912600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:11895400-11906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:11895400-11914400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:11895600-11908800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:11896000-11906200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr12:11897000-11905400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:11897000-11906400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:11897000-11906400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:11897000-11908800	Weak transcription	Brain Anterior Caudate	brain
25	chr12:11897200-11905400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:11897800-11905200	Weak transcription	Esophagus	oesophagus
27	chr12:11897800-11905400	Weak transcription	Aorta	Aorta
28	chr12:11898400-11905400	Weak transcription	Fetal Brain Male	brain
29	chr12:11898800-11905200	Weak transcription	Fetal Stomach	stomach
30	chr12:11899200-11904800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:11899200-11905200	Weak transcription	Placenta	Placenta
32	chr12:11899200-11905200	Weak transcription	Left Ventricle	heart
33	chr12:11899200-11905600	Weak transcription	Primary T cells from cord blood	blood
34	chr12:11899400-11905200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:11899400-11905400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:11899400-11905400	Weak transcription	Gastric	stomach
37	chr12:11899400-11905400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:11899400-11905400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:11899400-11908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:11899400-11908200	Weak transcription	HSMMtube	muscle
41	chr12:11899400-11908400	Weak transcription	HSMM	muscle
42	chr12:11899600-11905200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:11899600-11906000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:11899600-11906800	Weak transcription	NH-A	brain
45	chr12:11900000-11905000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:11900000-11905400	Weak transcription	Osteobl	bone
47	chr12:11900000-11907000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr12:11900200-11905400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:11900200-11906000	Weak transcription	Right Atrium	heart
50	chr12:11900400-11905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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