Variant report

Variant	rs9382631
Chromosome Location	chr6:56322389-56322390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs11751569	0.82[YRI][hapmap]
rs11753813	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs11756977	0.83[MEX][hapmap]
rs11757910	0.80[YRI][hapmap]
rs11757941	0.82[YRI][hapmap]
rs11758339	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11759493	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11961668	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12174955	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13204556	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13218268	0.82[YRI][hapmap]
rs1359068	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359070	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535610	0.93[ASN][1000 genomes]
rs1535612	0.93[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs1570492	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825773	0.89[MEX][hapmap]
rs2273972	0.86[CEU][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273973	0.93[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs2273974	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294697	0.82[YRI][hapmap]
rs2397221	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs2397226	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2894837	0.82[CHB][hapmap];0.94[MEX][hapmap];0.80[ASN][1000 genomes]
rs34954984	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35671304	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35926142	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3927453	0.85[ASN][1000 genomes]
rs4130060	0.90[CEU][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.82[ASN][1000 genomes]
rs4143828	0.90[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs4236139	0.91[GIH][hapmap];0.88[MEX][hapmap]
rs4236140	0.90[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap]
rs4236141	0.93[JPT][hapmap]
rs4236144	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs4236145	0.90[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4283892	0.90[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4331988	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4454141	0.89[GIH][hapmap];0.94[MEX][hapmap]
rs4499917	0.90[CEU][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs4544910	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45486696	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712132	0.90[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4712133	0.84[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4715625	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4715626	0.91[GIH][hapmap];0.94[MEX][hapmap]
rs4715627	0.91[GIH][hapmap];0.88[MEX][hapmap]
rs4715629	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs4715630	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs4715631	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs59101638	0.92[ASN][1000 genomes]
rs594435	0.84[JPT][hapmap]
rs595238	0.91[YRI][hapmap]
rs636389	1.00[ASW][hapmap];0.91[YRI][hapmap]
rs6459161	0.86[CEU][hapmap];0.93[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6459163	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs656550	0.81[CEU][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs656988	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6904202	0.91[GIH][hapmap];0.85[TSI][hapmap]
rs6911502	1.00[ASW][hapmap];0.81[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6913572	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914325	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6916287	0.81[ASN][1000 genomes]
rs6919608	0.91[GIH][hapmap]
rs6927258	0.95[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6928601	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs721475	0.94[ASN][1000 genomes]
rs72877350	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7741295	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7746753	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7755220	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7755361	0.82[CEU][hapmap]
rs7759875	0.84[CEU][hapmap]
rs7760640	0.82[CEU][hapmap]
rs7761281	0.80[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs7762629	0.80[CEU][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs7775847	0.82[YRI][hapmap]
rs9296848	0.87[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296850	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs9349822	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9349823	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349824	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349825	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9357921	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9357922	0.93[JPT][hapmap]
rs9370531	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370533	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs9370534	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370535	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382635	0.93[ASN][1000 genomes]
rs9396210	0.81[ASN][1000 genomes]
rs9396211	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9396213	0.82[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9396214	0.86[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9396215	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9396218	0.93[ASN][1000 genomes]
rs9464389	0.83[ASN][1000 genomes]
rs9475709	0.95[ASN][1000 genomes]
rs9475713	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs9475714	0.91[GIH][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9382631	TRAM2	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56309400-56322600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:56313200-56323800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:56314400-56323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:56315000-56347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:56315000-56349800	Strong transcription	HSMM	muscle
7	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56315800-56323400	Weak transcription	Aorta	Aorta
9	chr6:56315800-56329200	Weak transcription	Small Intestine	intestine
10	chr6:56316000-56323400	Weak transcription	Gastric	stomach
11	chr6:56316000-56323800	Weak transcription	Right Ventricle	heart
12	chr6:56316400-56322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:56316400-56323800	Weak transcription	Fetal Intestine Small	intestine
14	chr6:56316600-56323000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:56316600-56323200	Weak transcription	Ovary	ovary
16	chr6:56316600-56323200	Weak transcription	Pancreas	Pancrea
17	chr6:56316600-56323400	Weak transcription	Fetal Stomach	stomach
18	chr6:56316800-56322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:56316800-56322800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:56316800-56323600	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:56316800-56337600	Weak transcription	Hela-S3	cervix
22	chr6:56317200-56322800	Weak transcription	HepG2	liver
23	chr6:56317200-56323200	Weak transcription	Fetal Heart	heart
24	chr6:56317200-56342800	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr6:56317600-56324200	Weak transcription	Brain Angular Gyrus	brain
26	chr6:56317800-56322600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:56317800-56331200	Strong transcription	HSMMtube	muscle
28	chr6:56318000-56323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:56318000-56323400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:56318000-56340600	Strong transcription	Fetal Intestine Large	intestine
31	chr6:56318400-56322800	Weak transcription	Fetal Brain Female	brain
32	chr6:56318400-56323000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:56318600-56323000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:56318600-56331000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:56318800-56325200	Strong transcription	HUVEC	blood vessel
36	chr6:56318800-56325800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:56318800-56332000	Strong transcription	Fetal Lung	lung
38	chr6:56319000-56325800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:56319000-56326000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:56319000-56331200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:56319000-56348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:56319200-56331200	Strong transcription	Osteobl	bone
43	chr6:56319200-56340400	Strong transcription	NH-A	brain
44	chr6:56319200-56348400	Strong transcription	NHDF-Ad	bronchial
45	chr6:56319400-56329200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:56319400-56343600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:56319400-56344200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:56319600-56323400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:56319800-56322800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr6:56320000-56323000	Weak transcription	HMEC	breast

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