Variant report

Variant	rs9821630
Chromosome Location	chr3:16970938-16970939
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	chr3:16967326..16970983-chr3:16976551..16980496,4	K562	blood:
2	chr3:16967326..16970983-chr3:16976849..16980496,3	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1025818	0.83[ASN][1000 genomes]
rs10865746	0.80[JPT][hapmap]
rs11128810	0.82[ASN][1000 genomes]
rs11128813	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11128814	0.82[ASN][1000 genomes]
rs11717433	0.88[ASN][1000 genomes]
rs11717649	0.83[ASN][1000 genomes]
rs11915356	0.86[ASN][1000 genomes]
rs12108065	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12233492	0.85[JPT][hapmap]
rs12488103	0.87[ASN][1000 genomes]
rs12491516	0.82[ASN][1000 genomes]
rs12492983	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12494582	0.82[ASN][1000 genomes]
rs12495362	0.90[ASN][1000 genomes]
rs13080108	0.81[JPT][hapmap]
rs1372071	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17042909	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17042920	0.89[ASN][1000 genomes]
rs1806555	0.85[JPT][hapmap]
rs1806556	0.80[JPT][hapmap]
rs2014490	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2197017	0.81[ASN][1000 genomes]
rs34322012	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3796299	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs3906814	0.89[JPT][hapmap]
rs4131153	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4289331	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4334629	0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4353792	0.81[JPT][hapmap]
rs4383507	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4402923	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4416363	0.88[ASN][1000 genomes]
rs4452313	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4472039	0.81[JPT][hapmap]
rs4577450	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4684305	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4684306	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4684307	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4684308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4685405	0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs4685411	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4685418	0.81[JPT][hapmap]
rs4685419	0.86[ASN][1000 genomes]
rs4685423	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4685424	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4685425	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4685426	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs58679681	0.88[ASN][1000 genomes]
rs58750701	0.85[ASN][1000 genomes]
rs58765457	0.83[ASN][1000 genomes]
rs62246033	0.88[ASN][1000 genomes]
rs62247183	0.83[ASN][1000 genomes]
rs62247186	0.84[ASN][1000 genomes]
rs62247190	0.83[ASN][1000 genomes]
rs6796352	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6803135	0.83[ASN][1000 genomes]
rs6806862	0.88[ASN][1000 genomes]
rs7612044	0.87[CHB][hapmap]
rs7617779	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7634374	0.81[ASN][1000 genomes]
rs7639882	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7648912	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7653834	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs964576	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9824172	0.87[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9825009	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9844888	0.91[JPT][hapmap]
rs9853476	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9879150	0.87[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9883633	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	21833088	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9821630	TMEM43	cis	cerebellum	SCAN
rs9821630	CHCHD4	cis	parietal	SCAN
rs9821630	COLQ	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16958000-16981800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:16959400-16986600	Weak transcription	Aorta	Aorta
3	chr3:16965000-16979000	Weak transcription	Lung	lung
4	chr3:16966800-16971800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:16967000-16985000	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:16967600-16977200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:16967800-16977800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:16968400-16973200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:16968600-16971800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:16968800-16971600	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:16968800-16972400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:16968800-16974000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:16969000-16971400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:16969000-16971400	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:16969000-16971600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:16969000-16971800	Enhancers	Psoas Muscle	Psoas
17	chr3:16969000-16972600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr3:16969000-16972600	Enhancers	Right Ventricle	heart
19	chr3:16969000-16972600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:16969000-16974000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:16969000-16977400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr3:16969200-16971400	Enhancers	Small Intestine	intestine
23	chr3:16969200-16971600	Enhancers	Left Ventricle	heart
24	chr3:16969200-16972200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr3:16969200-16972600	Enhancers	Right Atrium	heart
26	chr3:16969200-16972800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:16969200-16973600	Enhancers	Fetal Heart	heart
28	chr3:16969400-16971000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr3:16969400-16972600	Enhancers	Ovary	ovary
30	chr3:16969600-16971000	Weak transcription	Stomach Mucosa	stomach
31	chr3:16969600-16971600	Weak transcription	Brain Angular Gyrus	brain
32	chr3:16969600-16971600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:16969600-16977400	Weak transcription	Fetal Thymus	thymus
34	chr3:16969800-16971000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:16969800-16971200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:16969800-16971400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:16970000-16971000	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:16970000-16973000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:16970000-16977000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:16970200-16971400	Weak transcription	Placenta	Placenta
41	chr3:16970200-16971600	Enhancers	Adipose Nuclei	Adipose
42	chr3:16970200-16974200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:16970200-16974600	Weak transcription	Gastric	stomach
44	chr3:16970200-16975600	Weak transcription	Pancreas	Pancrea
45	chr3:16970400-16971000	Weak transcription	Primary T cells from cord blood	blood
46	chr3:16970400-16971000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:16970400-16971000	Weak transcription	Spleen	Spleen
48	chr3:16970400-16972400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:16970400-16977400	Weak transcription	Thymus	Thymus
50	chr3:16970800-16971000	Enhancers	Duodenum Mucosa	Duodenum

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