Variant report

Variant	rs17026756
Chromosome Location	chr2:86154004-86154005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86147713..86150880-chr2:86153499..86156772,3	K562	blood:
2	chr2:86149476..86151149-chr2:86152541..86154219,2	MCF-7	breast:
3	chr2:86146663..86150858-chr2:86151745..86155490,4	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10179419	0.81[JPT][hapmap]
rs10181978	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185207	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185280	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10192998	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10193207	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025704	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025705	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025706	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025707	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025708	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496319	0.81[JPT][hapmap]
rs11681961	0.81[JPT][hapmap]
rs11682312	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693421	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693423	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693435	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478916	0.81[CEU][hapmap]
rs12613609	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs12616165	0.90[AMR][1000 genomes]
rs12714154	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs12714157	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714158	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020072	0.81[JPT][hapmap]
rs13025142	0.84[CEU][hapmap]
rs13401298	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13422640	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs1401383	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap]
rs1401385	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs1438156	0.92[AMR][1000 genomes]
rs1518990	0.81[JPT][hapmap]
rs1533605	0.84[CEU][hapmap]
rs17026684	0.81[JPT][hapmap]
rs17026750	0.84[AMR][1000 genomes]
rs1866244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008559	0.93[AMR][1000 genomes]
rs2030275	0.81[JPT][hapmap]
rs2083170	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2164878	0.93[AMR][1000 genomes]
rs2176627	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2280316	0.81[JPT][hapmap]
rs2366947	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs2366950	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2679722	0.82[AMR][1000 genomes]
rs2945824	0.82[AMR][1000 genomes]
rs4331504	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4553826	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs4613279	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832015	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs4832017	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4832213	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs4832219	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs4832222	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832227	0.93[ASN][1000 genomes]
rs6547637	0.84[CEU][hapmap]
rs6547647	0.92[AMR][1000 genomes]
rs6714363	0.86[JPT][hapmap]
rs6716233	0.81[JPT][hapmap]
rs6718537	0.91[AMR][1000 genomes]
rs6721125	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs6726662	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6733593	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6734488	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs6753350	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs71411844	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561062	0.81[JPT][hapmap]
rs7576135	0.90[AMR][1000 genomes]
rs7586560	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs893445	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs893447	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893448	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309626	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17026756	IMMT	cis	cerebellum	SCAN
rs17026756	PTCD3	cis	cerebellum	SCAN
rs17026756	ST3GAL5	cis	cerebellum	SCAN
rs17026756	KCMF1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86142200-86155800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:86142400-86157800	Weak transcription	Aorta	Aorta
3	chr2:86147200-86155000	Enhancers	Brain Hippocampus Middle	brain
4	chr2:86148600-86156200	Weak transcription	NH-A	brain
5	chr2:86149400-86157400	Weak transcription	Pancreas	Pancrea
6	chr2:86149800-86157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:86149800-86157400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:86150400-86155000	Enhancers	Brain Substantia Nigra	brain
9	chr2:86150400-86155200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr2:86150400-86155200	Enhancers	A549	lung
11	chr2:86150800-86155000	Enhancers	Brain Cingulate Gyrus	brain
12	chr2:86151000-86154800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:86151000-86155000	Enhancers	Brain Angular Gyrus	brain
14	chr2:86151600-86155000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:86151600-86155200	Enhancers	Brain Anterior Caudate	brain
16	chr2:86151600-86156400	Enhancers	Placenta	Placenta
17	chr2:86151800-86155200	Enhancers	Spleen	Spleen
18	chr2:86152000-86154400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:86152200-86154800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:86152200-86163400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:86152400-86154800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:86152400-86155200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:86152400-86156200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:86152400-86163000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:86152600-86154200	Weak transcription	HSMM	muscle
26	chr2:86152600-86154400	Weak transcription	Gastric	stomach
27	chr2:86152800-86154200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:86152800-86161000	Weak transcription	Liver	Liver
29	chr2:86152800-86162400	Weak transcription	Right Atrium	heart
30	chr2:86153000-86156200	Weak transcription	Ovary	ovary
31	chr2:86153000-86157200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:86153200-86154200	Weak transcription	Fetal Thymus	thymus
33	chr2:86153200-86154600	Weak transcription	Left Ventricle	heart
34	chr2:86153200-86154600	Weak transcription	Lung	lung
35	chr2:86153200-86157200	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:86153400-86158800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:86153600-86154400	Enhancers	Stomach Mucosa	stomach
38	chr2:86153600-86154600	Enhancers	NHEK	skin
39	chr2:86153600-86154800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:86153600-86154800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:86153800-86154400	Flanking Active TSS	Hela-S3	cervix
42	chr2:86153800-86154600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:86153800-86154800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:86153800-86154800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:86153800-86154800	Enhancers	Adipose Nuclei	Adipose
46	chr2:86153800-86154800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:86153800-86154800	Weak transcription	Right Ventricle	heart
48	chr2:86153800-86154800	Enhancers	HMEC	breast
49	chr2:86153800-86154800	Enhancers	Osteobl	bone
50	chr2:86153800-86155200	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links