Variant report

Variant	rs6933547
Chromosome Location	chr6:37969064-37969065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11759458	0.82[YRI][hapmap]
rs11964613	1.00[YRI][hapmap]
rs11964671	1.00[YRI][hapmap]
rs12191440	0.87[CHB][hapmap]
rs12194872	0.87[CHB][hapmap]
rs12196555	0.87[CHB][hapmap]
rs12524157	0.87[CHB][hapmap]
rs13205214	0.81[YRI][hapmap]
rs13207526	1.00[YRI][hapmap]
rs1390735	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs1472364	0.87[CHB][hapmap]
rs16890185	0.82[YRI][hapmap]
rs16890194	1.00[YRI][hapmap]
rs2453882	1.00[YRI][hapmap]
rs2645096	0.85[YRI][hapmap]
rs2645098	0.95[YRI][hapmap]
rs2645104	1.00[YRI][hapmap]
rs2645115	1.00[YRI][hapmap]
rs2645126	1.00[YRI][hapmap]
rs2842499	0.96[YRI][hapmap]
rs2842514	1.00[YRI][hapmap]
rs2842516	1.00[YRI][hapmap]
rs2842524	1.00[YRI][hapmap]
rs4711518	1.00[YRI][hapmap]
rs4711519	0.87[CHB][hapmap]
rs6908106	0.82[YRI][hapmap]
rs6910837	1.00[YRI][hapmap]
rs6911481	0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2753764	chr6:37963308-37978172	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv34450	chr6:37963308-38007241	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6933547	MDGA1	cis	cerebellum	SCAN
rs6933547	C6orf126	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37956200-37978800	Weak transcription	Primary T cells from cord blood	blood
2	chr6:37957800-37976400	Weak transcription	Aorta	Aorta
3	chr6:37959400-37975600	Weak transcription	Left Ventricle	heart
4	chr6:37960800-37982400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:37962000-37973200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:37962200-37975800	Weak transcription	Liver	Liver
7	chr6:37963000-37969400	Weak transcription	Osteobl	bone
8	chr6:37963000-37973400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:37963000-37973400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:37963000-37975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:37963000-37975800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:37963000-37977600	Weak transcription	Ovary	ovary
13	chr6:37963000-37984800	Weak transcription	Right Atrium	heart
14	chr6:37963000-37995600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:37965600-37982200	Weak transcription	Psoas Muscle	Psoas
16	chr6:37965800-37979000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:37967600-37977600	Weak transcription	Primary B cells from cord blood	blood
18	chr6:37968600-37969400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr6:37968800-37969600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:37968800-37969600	Enhancers	Fetal Lung	lung
21	chr6:37969000-37969200	Enhancers	Fetal Kidney	kidney
22	chr6:37969000-37969400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:37969000-37969400	Enhancers	Brain Cingulate Gyrus	brain
24	chr6:37969000-37969400	Enhancers	Colon Smooth Muscle	Colon
25	chr6:37969000-37969400	Enhancers	Fetal Heart	heart
26	chr6:37969000-37969400	Enhancers	Fetal Intestine Small	intestine
27	chr6:37969000-37969600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:37969000-37969600	Enhancers	Brain Hippocampus Middle	brain
29	chr6:37969000-37969600	Enhancers	Brain Substantia Nigra	brain

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