Variant report

Variant	rs11756977
Chromosome Location	chr6:56420538-56420539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11753813	0.91[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs11758339	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs11759493	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs12527139	0.81[AMR][1000 genomes]
rs13194746	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13219448	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1535612	0.91[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs16887974	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17825773	0.84[MEX][hapmap]
rs2064591	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273972	0.82[GIH][hapmap];0.84[MEX][hapmap]
rs2273973	0.91[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs4130060	0.80[AMR][1000 genomes]
rs4143827	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143828	0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4236139	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4236140	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4236141	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4236142	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4236143	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4236144	0.81[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4236145	0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4283892	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs4329120	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4346846	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4454141	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4466244	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4472350	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4473850	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4499917	0.84[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes]
rs4712132	0.83[ASW][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4712133	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715626	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715627	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715628	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4715629	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715630	0.91[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4715631	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459161	0.81[CEU][hapmap];0.82[GIH][hapmap];0.88[MEX][hapmap]
rs6904202	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs6906792	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6907917	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6911502	0.83[MEX][hapmap]
rs6914184	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6919608	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6922770	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939305	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71549713	0.80[AMR][1000 genomes]
rs7741295	0.84[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs7743011	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7755361	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7755573	0.90[AMR][1000 genomes]
rs7758054	0.81[AMR][1000 genomes]
rs7759875	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760640	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7760695	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7761281	0.94[ASW][hapmap];0.86[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7762629	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9296848	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs9296849	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296850	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9349826	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9357921	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9357922	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9370533	0.84[CEU][hapmap]
rs9396213	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs9396214	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs9396220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464389	0.80[AMR][1000 genomes]
rs9475713	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9475714	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	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	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11756977	DST	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56408200-56440400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:56408200-56440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:56408200-56496000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:56408400-56430800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:56413800-56458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr6:56415400-56427000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:56415800-56426000	Weak transcription	Ovary	ovary
8	chr6:56415800-56435200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:56416000-56421000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:56416200-56420800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:56416200-56423000	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:56416400-56424200	Strong transcription	GM12878-XiMat	blood
13	chr6:56416400-56426800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:56416400-56427000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:56416800-56420600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:56417000-56427800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:56417000-56516400	Weak transcription	Pancreas	Pancrea
18	chr6:56417200-56462000	Weak transcription	Lung	lung
19	chr6:56417200-56481400	Weak transcription	Esophagus	oesophagus
20	chr6:56417400-56420600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:56417400-56420800	Strong transcription	Adipose Nuclei	Adipose
22	chr6:56417400-56422200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:56417400-56426400	Strong transcription	HMEC	breast
24	chr6:56417400-56430000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:56417400-56435400	Weak transcription	HepG2	liver
26	chr6:56417600-56426800	Strong transcription	Liver	Liver
27	chr6:56417800-56426800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:56417800-56430400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:56417800-56454200	Weak transcription	Psoas Muscle	Psoas
30	chr6:56417800-56455400	Weak transcription	Gastric	stomach
31	chr6:56418000-56430200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:56418000-56435400	Weak transcription	Fetal Brain Male	brain
33	chr6:56418200-56420600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:56418200-56426400	Strong transcription	NHDF-Ad	bronchial
35	chr6:56418200-56430800	Weak transcription	NHLF	lung
36	chr6:56418400-56423600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:56418400-56426400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:56418400-56426400	Strong transcription	NH-A	brain
39	chr6:56418400-56427000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:56418800-56427200	Strong transcription	Osteobl	bone
41	chr6:56419000-56420600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:56419000-56420600	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr6:56419200-56420600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:56419400-56420600	Strong transcription	H9 Cell Line	embryonic stem cell
45	chr6:56419400-56420600	Strong transcription	Fetal Brain Female	brain
46	chr6:56419400-56420800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr6:56419600-56420600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:56419600-56420600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr6:56419600-56420800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:56419600-56421000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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