Variant report

Variant	rs2748169
Chromosome Location	chr6:38534608-38534609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12525759	0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13219887	0.81[CHD][hapmap]
rs16890826	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16890840	0.83[JPT][hapmap];0.93[MEX][hapmap]
rs1699013	0.94[JPT][hapmap]
rs1699020	0.94[JPT][hapmap]
rs1739625	1.00[JPT][hapmap]
rs1781741	0.89[JPT][hapmap]
rs2748166	0.89[JPT][hapmap]
rs2748168	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2814891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2814893	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4316001	0.85[CEU][hapmap]
rs62396459	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62399160	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7769186	0.83[JPT][hapmap]

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	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
2	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
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2748169	ZNF76	cis	parietal	SCAN
rs2748169	MYO19	trans	brain	seeQTL
rs2748169	GLO1	cis	parietal	SCAN
rs2748169	ANKS1A	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:38513000-38539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:38514200-38539400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:38515600-38535800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:38516000-38538800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:38517800-38535000	Weak transcription	Brain Substantia Nigra	brain
10	chr6:38519200-38538800	Weak transcription	Primary T cells from cord blood	blood
11	chr6:38519200-38539400	Weak transcription	Left Ventricle	heart
12	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:38522800-38534800	Weak transcription	Fetal Heart	heart
14	chr6:38522800-38535200	Weak transcription	Psoas Muscle	Psoas
15	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
16	chr6:38523200-38534800	Weak transcription	NHLF	lung
17	chr6:38524000-38537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:38524000-38539200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr6:38532200-38539600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:38532400-38547800	Weak transcription	Fetal Kidney	kidney
21	chr6:38532800-38538200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:38533000-38544000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:38533200-38537800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:38533200-38547000	Weak transcription	Aorta	Aorta
25	chr6:38533400-38536200	Enhancers	Brain Germinal Matrix	brain
26	chr6:38533600-38536400	Enhancers	Fetal Brain Male	brain
27	chr6:38533800-38535600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:38533800-38536200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:38534000-38535600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:38534000-38535600	Enhancers	HUVEC	blood vessel
31	chr6:38534000-38536000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:38534000-38539200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:38534200-38534800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr6:38534200-38534800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr6:38534200-38534800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr6:38534200-38535000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr6:38534200-38535400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr6:38534200-38535800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:38534200-38535800	Enhancers	NH-A	brain
40	chr6:38534200-38536000	Enhancers	Fetal Brain Female	brain
41	chr6:38534200-38536400	Enhancers	Brain Angular Gyrus	brain
42	chr6:38534200-38536400	Enhancers	NHDF-Ad	bronchial
43	chr6:38534200-38539600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:38534200-38544800	Weak transcription	Fetal Intestine Large	intestine
45	chr6:38534400-38535400	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:38534400-38535600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:38534400-38535600	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:38534400-38535600	Enhancers	Brain Hippocampus Middle	brain
49	chr6:38534400-38535600	Enhancers	HSMM	muscle
50	chr6:38534400-38535800	Enhancers	Fetal Lung	lung

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