Variant report

Variant	rs1570492
Chromosome Location	chr6:56325895-56325896
allele	C/G
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	0.93[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];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11759493	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11961668	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12174955	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13204556	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13218268	0.82[YRI][hapmap]
rs1359068	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1359070	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535610	0.93[ASN][1000 genomes]
rs1535612	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[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];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273973	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]
rs2273974	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294697	0.82[YRI][hapmap]
rs2397221	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs2397226	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2894837	0.88[CHB][hapmap];0.94[MEX][hapmap];0.80[ASN][1000 genomes]
rs34954984	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35671304	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35926142	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3927453	0.85[ASN][1000 genomes]
rs4130060	0.90[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.82[ASN][1000 genomes]
rs4143828	0.90[CEU][hapmap];0.87[CHB][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	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs4236144	0.90[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4236145	0.90[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4283892	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4331988	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4454141	0.89[GIH][hapmap];0.94[MEX][hapmap]
rs4499917	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs4544910	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs45486696	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712132	0.90[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4712133	0.87[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs4715625	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[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];0.87[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][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];0.87[CHB][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6459163	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs656550	0.81[CEU][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs656988	0.81[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.92[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];0.82[CHB][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6913572	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914325	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6916287	0.81[ASN][1000 genomes]
rs6919608	0.91[GIH][hapmap]
rs6927258	0.95[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6928601	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs721475	0.94[ASN][1000 genomes]
rs72877350	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7741295	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7746753	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7755220	0.88[AMR][1000 genomes];1.00[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];0.87[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs7762629	0.80[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap]
rs7775847	0.82[YRI][hapmap]
rs9296848	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296850	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap]
rs9349822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9349823	1.00[CEU][hapmap];0.93[CHB][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349824	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9349825	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9357921	0.87[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9357922	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs9370531	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370533	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs9370534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9370535	0.90[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9382631	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382635	0.93[ASN][1000 genomes]
rs9396210	0.81[ASN][1000 genomes]
rs9396211	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9396213	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9396214	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9396215	0.83[AMR][1000 genomes];0.82[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
rs1570492	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	chr6:56315000-56347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:56315000-56349800	Strong transcription	HSMM	muscle
4	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:56315800-56329200	Weak transcription	Small Intestine	intestine
6	chr6:56316800-56337600	Weak transcription	Hela-S3	cervix
7	chr6:56317200-56342800	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr6:56317800-56331200	Strong transcription	HSMMtube	muscle
9	chr6:56318000-56340600	Strong transcription	Fetal Intestine Large	intestine
10	chr6:56318600-56331000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:56318800-56332000	Strong transcription	Fetal Lung	lung
12	chr6:56319000-56326000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:56319000-56331200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:56319000-56348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:56319200-56331200	Strong transcription	Osteobl	bone
16	chr6:56319200-56340400	Strong transcription	NH-A	brain
17	chr6:56319200-56348400	Strong transcription	NHDF-Ad	bronchial
18	chr6:56319400-56329200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:56319400-56343600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:56319400-56344200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:56320000-56338800	Strong transcription	Liver	Liver
22	chr6:56320800-56328600	Strong transcription	Brain Substantia Nigra	brain
23	chr6:56320800-56331200	Strong transcription	Brain Anterior Caudate	brain
24	chr6:56321000-56331000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr6:56321000-56331200	Strong transcription	Fetal Muscle Leg	muscle
26	chr6:56321000-56331200	Strong transcription	Left Ventricle	heart
27	chr6:56321000-56331800	Strong transcription	Brain Hippocampus Middle	brain
28	chr6:56321000-56343400	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:56321200-56343800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:56321800-56331800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:56322000-56326600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:56322000-56330000	Strong transcription	Brain Cingulate Gyrus	brain
33	chr6:56322000-56330800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr6:56322000-56331600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:56322000-56332400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr6:56322200-56331400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr6:56322200-56332200	Strong transcription	GM12878-XiMat	blood
38	chr6:56322200-56339000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:56322200-56349200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:56322400-56344200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:56322600-56348200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:56322800-56331000	Strong transcription	HepG2	liver
43	chr6:56323000-56326400	Strong transcription	Rectal Smooth Muscle	rectum
44	chr6:56323000-56331800	Strong transcription	HMEC	breast
45	chr6:56323600-56331200	Strong transcription	Colon Smooth Muscle	Colon
46	chr6:56324000-56333600	Weak transcription	Psoas Muscle	Psoas
47	chr6:56324200-56327200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:56324200-56327200	Weak transcription	Colonic Mucosa	Colon
49	chr6:56324200-56329200	Weak transcription	Esophagus	oesophagus
50	chr6:56324200-56331200	Strong transcription	Brain Angular Gyrus	brain

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