Variant report

Variant	rs6905637
Chromosome Location	chr6:38277910-38277911
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:38275306..38278894-chr6:38287022..38290918,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1475761	0.96[CEU][hapmap]
rs1931767	0.96[CEU][hapmap];0.83[TSI][hapmap]
rs228181	1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs228182	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs228184	0.86[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs228185	0.96[CEU][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs228187	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs4711533	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714136	0.95[CEU][hapmap]
rs4714140	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4714144	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922620	0.95[CEU][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs7760807	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349067	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380737	0.87[CEU][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap]
rs9470847	0.96[CEU][hapmap]
rs9470848	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs9470851	0.96[CEU][hapmap]
rs9470856	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6905637	C6orf64	cis	cerebellum	SCAN
rs6905637	C6orf129	cis	parietal	SCAN
rs6905637	C6orf106	cis	parietal	SCAN
rs6905637	SPTLC3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38274400-38288600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:38275400-38301200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:38276000-38286200	Weak transcription	Primary T cells from cord blood	blood
4	chr6:38276000-38287600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:38276000-38287800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:38276200-38286800	Weak transcription	HSMMtube	muscle
7	chr6:38277600-38278200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:38277600-38278200	Enhancers	GM12878-XiMat	blood
9	chr6:38277600-38278400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:38277800-38278000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:38277800-38278000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr6:38277800-38278000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:38277800-38278000	Enhancers	Gastric	stomach
14	chr6:38277800-38278000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr6:38277800-38278200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:38277800-38278200	Enhancers	Lung	lung
17	chr6:38277800-38278200	Enhancers	Right Atrium	heart
18	chr6:38277800-38278200	Enhancers	Right Ventricle	heart
19	chr6:38277800-38278200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr6:38277800-38278800	Enhancers	Psoas Muscle	Psoas
21	chr6:38277800-38279000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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