Variant report

Variant	rs10485555
Chromosome Location	chr20:16506321-16506322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1008506	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10485553	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10485556	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12479497	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12480660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555195	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17671618	1.00[JPT][hapmap]
rs17672161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17673447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17673673	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740473	0.86[AFR][1000 genomes]
rs17741318	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741475	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1998085	1.00[JPT][hapmap]
rs2143983	0.85[CEU][hapmap]
rs2144896	1.00[JPT][hapmap];0.86[AFR][1000 genomes]
rs2180472	0.86[AFR][1000 genomes]
rs34122290	0.86[AFR][1000 genomes]
rs34550969	0.86[AFR][1000 genomes]
rs34761754	0.86[AFR][1000 genomes]
rs41306902	0.86[ASN][1000 genomes]
rs4813218	0.86[AFR][1000 genomes]
rs56072219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56363883	0.86[AFR][1000 genomes]
rs56402523	0.86[AFR][1000 genomes]
rs6034498	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6034499	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034506	0.85[CEU][hapmap]
rs6044009	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6044021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6044022	0.84[CEU][hapmap]
rs6044023	0.85[CEU][hapmap]
rs6044024	0.88[CEU][hapmap]
rs6044031	0.85[CEU][hapmap]
rs6044033	0.81[CEU][hapmap]
rs6044034	0.85[CEU][hapmap]
rs6044052	0.85[CEU][hapmap]
rs6044055	0.85[CEU][hapmap]
rs6080271	0.86[AFR][1000 genomes]
rs6080290	1.00[JPT][hapmap]
rs6080299	1.00[JPT][hapmap]
rs6111143	0.86[AFR][1000 genomes]
rs6131830	0.85[CEU][hapmap]
rs6135765	0.85[CEU][hapmap]
rs7262082	0.84[CEU][hapmap]
rs73597771	0.86[ASN][1000 genomes]
rs73597772	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73597773	0.86[ASN][1000 genomes]
rs73597774	0.86[ASN][1000 genomes]
rs8118656	1.00[JPT][hapmap];0.86[AFR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10485555	ZNF350	trans	brain	seeQTL
rs10485555	C20orf72	cis	parietal	SCAN
rs10485555	KIF16B	cis	cerebellum	SCAN
rs10485555	KIF16B	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16431400-16508200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:16453600-16508200	Weak transcription	Stomach Mucosa	stomach
3	chr20:16467000-16508800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr20:16467400-16507000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr20:16469600-16507600	Weak transcription	HSMMtube	muscle
6	chr20:16470200-16508600	Weak transcription	NHLF	lung
7	chr20:16472800-16517400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr20:16480600-16509400	Weak transcription	K562	blood
9	chr20:16482600-16507200	Weak transcription	HSMM	muscle
10	chr20:16485200-16508600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr20:16485600-16508000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr20:16485800-16521200	Weak transcription	Right Ventricle	heart
13	chr20:16488600-16507000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr20:16488600-16507200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr20:16488600-16507200	Weak transcription	Osteobl	bone
16	chr20:16488800-16508800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr20:16488800-16509200	Weak transcription	Small Intestine	intestine
18	chr20:16489000-16507200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr20:16489000-16511000	Weak transcription	Colonic Mucosa	Colon
20	chr20:16489200-16507000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr20:16489200-16508600	Weak transcription	HepG2	liver
22	chr20:16489200-16512200	Weak transcription	Gastric	stomach
23	chr20:16489200-16521000	Weak transcription	Spleen	Spleen
24	chr20:16489400-16507000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr20:16489400-16507800	Weak transcription	NHEK	skin
26	chr20:16489400-16510800	Weak transcription	Lung	lung
27	chr20:16489400-16517600	Weak transcription	Pancreas	Pancrea
28	chr20:16490400-16510200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr20:16491800-16507000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr20:16491800-16508600	Weak transcription	Fetal Kidney	kidney
31	chr20:16491800-16511000	Weak transcription	Esophagus	oesophagus
32	chr20:16492000-16508600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr20:16492000-16509800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr20:16492400-16508600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr20:16492400-16517800	Weak transcription	Colon Smooth Muscle	Colon
36	chr20:16492600-16528800	Weak transcription	Primary B cells from cord blood	blood
37	chr20:16493000-16507200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr20:16493000-16521200	Weak transcription	Liver	Liver
39	chr20:16493200-16507400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr20:16493200-16507600	Weak transcription	Left Ventricle	heart
41	chr20:16493600-16508800	Weak transcription	Fetal Lung	lung
42	chr20:16493600-16509400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr20:16493600-16516200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr20:16493800-16508200	Weak transcription	Psoas Muscle	Psoas
45	chr20:16496000-16509400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr20:16497000-16507600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr20:16497400-16507200	Weak transcription	Brain Anterior Caudate	brain
48	chr20:16497400-16507200	Weak transcription	Ovary	ovary
49	chr20:16497400-16509600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr20:16497600-16508400	Weak transcription	Fetal Brain Female	brain

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