Variant report

Variant	rs259678
Chromosome Location	chr6:37882780-37882781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11756656	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1212636	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12194872	0.83[TSI][hapmap]
rs12211975	0.84[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs1390735	0.81[TSI][hapmap]
rs174105	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs187741	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1885325	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1979759	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2055205	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2180514	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2201646	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2395687	0.85[ASN][1000 genomes]
rs259672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259674	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs259675	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs259676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259677	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259682	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs259683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs259685	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs259687	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs259688	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs259693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs259694	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs259714	0.81[ASN][1000 genomes]
rs259717	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs259721	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259722	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs259723	0.92[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs3792706	0.88[ASN][1000 genomes]
rs4142102	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs4711522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs4711523	0.90[CEU][hapmap];0.91[TSI][hapmap]
rs4711524	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4714118	0.90[ASN][1000 genomes]
rs4714123	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs6458030	0.84[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs6458036	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458040	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs67479083	0.92[ASN][1000 genomes]
rs6912097	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6915506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6917668	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6920185	0.88[ASN][1000 genomes]
rs6926280	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs6929371	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6930859	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs6934617	0.81[CEU][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6936504	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7765798	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9349053	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9369029	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9369033	0.83[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs9380703	1.00[CEU][hapmap]
rs9394469	0.88[ASN][1000 genomes]
rs9394471	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9462374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9462380	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9470714	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9470723	0.92[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9470724	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9470725	0.88[ASN][1000 genomes]
rs9470762	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs9647620	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv970036	chr6:37876765-37894762	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs259678	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37850600-37890400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37851000-37884600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:37857600-37886000	Weak transcription	Esophagus	oesophagus
4	chr6:37857600-37895400	Weak transcription	Pancreas	Pancrea
5	chr6:37862400-37884000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:37866000-37885600	Weak transcription	Hela-S3	cervix
7	chr6:37872000-37887600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:37872000-37888200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:37872000-37890400	Weak transcription	Small Intestine	intestine
10	chr6:37872200-37883000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:37872200-37884000	Weak transcription	Adipose Nuclei	Adipose
12	chr6:37872200-37884600	Weak transcription	Fetal Kidney	kidney
13	chr6:37872400-37883000	Weak transcription	Brain Substantia Nigra	brain
14	chr6:37872600-37885200	Weak transcription	HepG2	liver
15	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:37873200-37887400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:37874000-37888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:37874200-37884600	Weak transcription	A549	lung
20	chr6:37874400-37887600	Weak transcription	Spleen	Spleen
21	chr6:37874400-37888200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:37874600-37903800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr6:37876600-37903200	Weak transcription	Dnd41	blood
24	chr6:37877600-37882800	Weak transcription	Liver	Liver
25	chr6:37877600-37884000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:37878000-37883200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr6:37878000-37883200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:37878200-37883400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:37878200-37883800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:37878800-37900400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:37879600-37889600	Weak transcription	K562	blood
32	chr6:37879800-37886200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:37879800-37887400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:37879800-37887600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr6:37879800-37890400	Weak transcription	GM12878-XiMat	blood
36	chr6:37880000-37883200	Weak transcription	Psoas Muscle	Psoas
37	chr6:37880000-37883200	Weak transcription	HSMMtube	muscle
38	chr6:37880000-37885000	Weak transcription	Stomach Mucosa	stomach
39	chr6:37880000-37887600	Weak transcription	Right Atrium	heart
40	chr6:37880000-37888400	Weak transcription	Gastric	stomach
41	chr6:37880000-37888600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:37880000-37889600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:37880000-37890800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:37880000-37892200	Weak transcription	Ovary	ovary
45	chr6:37880000-37896600	Weak transcription	Right Ventricle	heart
46	chr6:37880000-37898000	Weak transcription	Fetal Thymus	thymus
47	chr6:37880200-37884200	Enhancers	NHEK	skin
48	chr6:37880200-37887400	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:37880200-37888200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:37880200-37930000	Weak transcription	Thymus	Thymus

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