Variant report

Variant	rs6929371
Chromosome Location	chr6:38081015-38081016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10755700	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12194872	0.83[TSI][hapmap]
rs13198420	0.86[CHB][hapmap]
rs1390735	0.81[TSI][hapmap]
rs1885325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1923279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1979759	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2201646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs259678	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]
rs259687	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4506034	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4711523	0.86[CEU][hapmap];0.91[TSI][hapmap]
rs4711524	0.82[EUR][1000 genomes]
rs4714123	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4714125	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6458040	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6458042	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916091	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6917668	1.00[YRI][hapmap]
rs6924634	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6930859	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6936504	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6938580	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7751390	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7765798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs881681	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9349053	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs9369029	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs9369033	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9380716	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394471	0.85[EUR][1000 genomes]
rs9462374	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9462380	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9470767	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470800	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	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
rs6929371	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38030800-38085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:38035000-38084000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:38046000-38084200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:38049400-38084400	Weak transcription	Hela-S3	cervix
6	chr6:38052800-38083800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:38052800-38084000	Weak transcription	Dnd41	blood
8	chr6:38053000-38084000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:38053000-38090400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:38053200-38084000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:38054400-38084000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:38054600-38084000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr6:38055600-38084400	Weak transcription	Adipose Nuclei	Adipose
14	chr6:38055800-38084200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:38057200-38109200	Weak transcription	K562	blood
16	chr6:38059800-38091600	Weak transcription	Spleen	Spleen
17	chr6:38060000-38092000	Weak transcription	Aorta	Aorta
18	chr6:38060000-38099400	Weak transcription	Right Ventricle	heart
19	chr6:38060000-38108200	Weak transcription	Ovary	ovary
20	chr6:38063400-38083600	Weak transcription	HepG2	liver
21	chr6:38063400-38085600	Weak transcription	A549	lung
22	chr6:38063800-38099000	Weak transcription	NH-A	brain
23	chr6:38068400-38083800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:38068400-38083800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:38068600-38084200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:38071800-38091400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:38072000-38085400	Weak transcription	GM12878-XiMat	blood
28	chr6:38072200-38108400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:38073000-38082400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr6:38073200-38081800	Weak transcription	NHEK	skin
31	chr6:38073200-38082400	Weak transcription	Small Intestine	intestine
32	chr6:38073400-38082200	Weak transcription	HMEC	breast
33	chr6:38073400-38084000	Weak transcription	HUVEC	blood vessel
34	chr6:38073600-38082800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:38074200-38086000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:38074600-38085800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:38074600-38086000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:38074800-38084200	Weak transcription	Placenta	Placenta
39	chr6:38075200-38084400	Weak transcription	Liver	Liver
40	chr6:38075200-38092000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:38075200-38118200	Weak transcription	Colonic Mucosa	Colon
42	chr6:38075400-38083600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:38075400-38084400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:38075400-38103800	Weak transcription	Pancreas	Pancrea
45	chr6:38076400-38082200	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:38076400-38091400	Strong transcription	Primary B cells from cord blood	blood
47	chr6:38076600-38082200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:38076600-38082200	Weak transcription	Right Atrium	heart
49	chr6:38076600-38084000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:38076600-38084200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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