Variant report

Variant	rs2201646
Chromosome Location	chr6:38008961-38008962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12194872	0.83[TSI][hapmap]
rs13198420	0.86[CHB][hapmap]
rs1390735	0.81[TSI][hapmap]
rs174105	0.83[ASN][1000 genomes]
rs187741	0.81[ASN][1000 genomes]
rs1885325	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1923279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1979759	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2055205	0.85[ASN][1000 genomes]
rs2180514	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs259672	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs259674	0.84[ASN][1000 genomes]
rs259675	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs259676	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs259677	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs259678	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]
rs259682	0.84[ASN][1000 genomes]
rs259683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs259685	0.83[ASN][1000 genomes]
rs259687	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs259688	0.81[ASN][1000 genomes]
rs259693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs259694	0.85[ASN][1000 genomes]
rs4506034	0.85[EUR][1000 genomes]
rs4711522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4711523	0.86[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs4711524	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4714118	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4714123	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4714125	0.86[EUR][1000 genomes]
rs6458036	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458040	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6458042	0.84[EUR][1000 genomes]
rs67479083	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6912097	0.82[EUR][1000 genomes]
rs6915506	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[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];0.82[EUR][1000 genomes]
rs6917668	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6920185	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6929371	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]
rs6930859	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6936504	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6938580	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs7751390	0.87[EUR][1000 genomes]
rs7765798	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881681	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9349053	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9369029	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9369033	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs9380716	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9394469	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9394471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462374	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9462380	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9470723	0.92[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9470724	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs9470762	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9470767	0.86[EUR][1000 genomes]
rs9470800	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9647620	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][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	esv2763549	chr6:37985025-38014006	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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
8	nsv970298	chr6:38003938-38014330	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2201646	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37985000-38030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:37994400-38011400	Weak transcription	Aorta	Aorta
3	chr6:37995800-38013000	Weak transcription	Fetal Thymus	thymus
4	chr6:37995800-38020600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:37996000-38015400	Weak transcription	HSMMtube	muscle
6	chr6:37998600-38029200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:37999800-38017600	Weak transcription	Right Atrium	heart
8	chr6:37999800-38018600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:38001000-38028600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:38002400-38029400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:38002800-38017800	Weak transcription	HSMM	muscle
12	chr6:38002800-38024400	Weak transcription	Fetal Stomach	stomach
13	chr6:38003000-38024800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:38003000-38025000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:38003200-38024400	Weak transcription	Primary T cells from cord blood	blood
16	chr6:38003600-38025400	Weak transcription	NHDF-Ad	bronchial
17	chr6:38003800-38017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:38004000-38011000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:38004000-38018000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:38004000-38018200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:38004200-38013600	Weak transcription	Small Intestine	intestine
22	chr6:38004200-38024600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:38004200-38029200	Weak transcription	Primary B cells from cord blood	blood
24	chr6:38006000-38011400	Weak transcription	Left Ventricle	heart
25	chr6:38006200-38010000	Weak transcription	Brain Substantia Nigra	brain
26	chr6:38006800-38011000	Weak transcription	Psoas Muscle	Psoas
27	chr6:38006800-38024200	Weak transcription	Thymus	Thymus
28	chr6:38007000-38009000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:38007200-38009000	Enhancers	HepG2	liver
30	chr6:38007400-38025400	Weak transcription	NH-A	brain
31	chr6:38007600-38018000	Weak transcription	Osteobl	bone
32	chr6:38007800-38010000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr6:38008400-38009000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:38008400-38009000	Enhancers	Fetal Lung	lung
35	chr6:38008400-38009000	Enhancers	A549	lung
36	chr6:38008400-38028400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:38008800-38009000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr6:38008800-38009000	Enhancers	Right Ventricle	heart
39	chr6:38008800-38013600	Weak transcription	Liver	Liver

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