Variant report

Variant	rs9376837
Chromosome Location	chr6:144999763-144999764
allele	A/C
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:33)

rs_ID	r²[population]
rs10499232	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11155364	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs11155365	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11155370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209027	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs12662483	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs12662875	0.82[ASN][1000 genomes]
rs17073972	0.83[JPT][hapmap]
rs17073995	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs17074004	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1980379	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2056744	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2056745	0.91[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap]
rs3950347	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4895646	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6907773	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9373419	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs9373420	0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376835	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9376838	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9386075	0.98[ASN][1000 genomes]
rs9386076	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9390184	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs9390187	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390188	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390194	0.82[CHB][hapmap]
rs9399483	0.91[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs9399485	0.98[ASN][1000 genomes]
rs9399486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399488	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9399489	1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9403572	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9403578	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv604822	chr6:144968195-145001887	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1032838	chr6:144978504-145110121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9376837	STX11	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144981200-145031000	Weak transcription	Placenta	Placenta
2	chr6:144982800-145010000	Weak transcription	Fetal Stomach	stomach
3	chr6:144983000-145024600	Weak transcription	Fetal Kidney	kidney
4	chr6:144985000-145004200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:144986200-145002000	Weak transcription	Small Intestine	intestine
6	chr6:144993000-145000800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:144995400-145002000	Weak transcription	Primary T cells from cord blood	blood
8	chr6:144995800-145001800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:144996000-145000000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:144996000-145010000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:144996600-145001600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:144996600-145001800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:144996600-145002000	Weak transcription	Lung	lung
14	chr6:144996600-145004000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:144996600-145004000	Weak transcription	Thymus	Thymus
16	chr6:144996600-145004200	Weak transcription	HSMMtube	muscle
17	chr6:144996600-145007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:144996600-145018400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:144996600-145052400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:144996800-145000800	Weak transcription	Ovary	ovary
21	chr6:144996800-145001000	Weak transcription	Fetal Thymus	thymus
22	chr6:144996800-145001600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:144996800-145002000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:144996800-145002000	Weak transcription	Right Atrium	heart
25	chr6:144996800-145002200	Weak transcription	Fetal Heart	heart
26	chr6:144996800-145007400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:144996800-145009800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:144997000-144999800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:144997000-145000000	Weak transcription	Adipose Nuclei	Adipose
30	chr6:144997000-145000200	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:144997000-145000200	Weak transcription	HSMM	muscle
32	chr6:144997000-145000400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:144997000-145000800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr6:144997000-145002000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:144997000-145002000	Weak transcription	Left Ventricle	heart
36	chr6:144997000-145002200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:144997000-145004000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:144997000-145004200	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:144997000-145004200	Weak transcription	Gastric	stomach
40	chr6:144997000-145004200	Weak transcription	Pancreas	Pancrea
41	chr6:144997000-145004200	Weak transcription	Psoas Muscle	Psoas
42	chr6:144997000-145004200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:144997000-145004200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:144997000-145006200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:144997000-145006400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:144997000-145006600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:144997000-145008000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr6:144997000-145008000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:144997000-145008600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:144997000-145009400	Weak transcription	HMEC	breast

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