Variant report

Variant	rs17818624
Chromosome Location	chr12:11896846-11896847
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1009951	0.82[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1009953	0.82[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1009954	0.92[CEU][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs10743967	0.93[EUR][1000 genomes]
rs10845407	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10845408	0.96[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11054421	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11054423	0.92[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs11054424	0.88[EUR][1000 genomes]
rs11054429	0.90[EUR][1000 genomes]
rs11054433	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11054439	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11615175	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12228191	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12369491	0.81[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12828066	0.86[CHB][hapmap]
rs17818461	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs17818498	0.96[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2051525	0.96[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2187642	0.96[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2416882	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs2416883	0.81[CEU][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs2724588	0.92[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs2724599	0.82[EUR][1000 genomes]
rs2724600	0.82[EUR][1000 genomes]
rs2724616	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2724618	0.92[EUR][1000 genomes]
rs2724633	0.92[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2724645	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs2724648	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2856321	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2856322	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2856324	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs2856338	0.89[CHD][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2856344	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs2860431	0.81[TSI][hapmap]
rs2900208	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2954980	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4763719	0.82[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4763720	0.82[EUR][1000 genomes]
rs4763721	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7488701	0.82[EUR][1000 genomes]
rs762717	0.82[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs972798	0.83[JPT][hapmap];0.83[TSI][hapmap];0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17818624	KLRA1	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11873200-11902400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:11873200-11909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:11882400-11899200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:11882400-11902600	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:11882400-11903200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:11883800-11906000	Weak transcription	Liver	Liver
7	chr12:11884200-11899000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:11885200-11906200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:11885600-11898600	Weak transcription	Primary T cells from cord blood	blood
10	chr12:11885600-11899000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:11885600-11905200	Weak transcription	Fetal Intestine Large	intestine
12	chr12:11885800-11898400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:11885800-11911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr12:11886000-11900000	Weak transcription	Colonic Mucosa	Colon
15	chr12:11886800-11897800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr12:11889800-11901800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:11890000-11902400	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:11892400-11898600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:11893200-11915000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:11893600-11897800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:11893800-11901200	Enhancers	HMEC	breast
22	chr12:11894400-11897800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr12:11894400-11898800	Weak transcription	Right Atrium	heart
24	chr12:11894400-11899000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:11894600-11897000	Weak transcription	Placenta	Placenta
26	chr12:11894600-11897000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:11894600-11897600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:11894600-11897800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:11894600-11898200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:11894600-11898200	Weak transcription	Gastric	stomach
31	chr12:11894600-11898400	Weak transcription	Pancreas	Pancrea
32	chr12:11894600-11898400	Weak transcription	NH-A	brain
33	chr12:11894600-11898600	Weak transcription	Osteobl	bone
34	chr12:11894600-11898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:11894600-11905200	Weak transcription	Fetal Intestine Small	intestine
36	chr12:11894600-11905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:11894600-11905400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr12:11894600-11906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:11894600-11908400	Weak transcription	Psoas Muscle	Psoas
40	chr12:11894800-11897400	Weak transcription	HUVEC	blood vessel
41	chr12:11894800-11899200	Weak transcription	HSMM	muscle
42	chr12:11894800-11906000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:11894800-11906600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:11895000-11897000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:11895000-11897400	Weak transcription	A549	lung
46	chr12:11895000-11897800	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:11895000-11898200	Weak transcription	Small Intestine	intestine
48	chr12:11895000-11899200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:11895000-11906000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:11895000-11906800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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