Variant report

Variant	rs6904492
Chromosome Location	chr6:140202223-140202224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139692335..139698075-chr6:140197375..140205470,17	MCF-7	breast:
2	chr6:140199686..140202479-chr6:140203984..140206544,2	K562	blood:
3	chr6:140202203..140203486-chr6:140248180..140248949,4	MCF-7	breast:
4	chr6:139692969..139697282-chr6:140197638..140202883,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2223966	0.94[ASN][1000 genomes]
rs581559	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs590585	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs590587	0.93[ASN][1000 genomes]
rs592755	0.94[ASN][1000 genomes]
rs606159	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608122	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs613274	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs618471	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627705	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs629778	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs633026	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs654917	0.93[ASN][1000 genomes]
rs7744208	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs7760148	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap]
rs9376477	0.85[JPT][hapmap];0.85[TSI][hapmap]
rs9376478	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv1017015	chr6:140084137-140300565	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019407	chr6:140087307-140304334	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140190800-140203400	Weak transcription	Fetal Lung	lung
2	chr6:140191600-140203000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:140194400-140203000	Weak transcription	NHLF	lung
4	chr6:140194800-140204200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:140199400-140202400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:140199400-140202600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:140201000-140206400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:140201200-140202400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:140201200-140203000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:140201200-140203200	Weak transcription	Placenta	Placenta
11	chr6:140201400-140202600	Weak transcription	Osteobl	bone
12	chr6:140201400-140203000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:140201400-140203000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:140201400-140203400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:140201400-140204200	Weak transcription	Liver	Liver
16	chr6:140201600-140203000	Weak transcription	K562	blood
17	chr6:140201800-140203200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:140201800-140203200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:140201800-140205000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr6:140201800-140206400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:140202000-140203200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:140202000-140203800	Enhancers	Brain Germinal Matrix	brain
23	chr6:140202000-140209000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:140202000-140209600	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:140202200-140202400	Enhancers	Fetal Kidney	kidney
26	chr6:140202200-140204400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:140202200-140205000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr6:140202200-140206400	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links