Variant report

Variant	rs12198642
Chromosome Location	chr6:140242291-140242292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140238724..140241294-chr6:140241796..140244314,2	K562	blood:
2	chr6:140241965..140244669-chr6:140782881..140785815,2	MCF-7	breast:
3	chr6:140240716..140243560-chr6:140261380..140263735,2	K562	blood:
4	chr6:139692913..139695578-chr6:140241310..140243689,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10457036	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10457699	1.00[JPT][hapmap]
rs10457701	0.90[ASN][1000 genomes]
rs10457702	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11155092	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155093	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155094	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754775	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193363	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193742	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194624	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194665	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198042	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198595	0.90[ASN][1000 genomes]
rs12198639	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202850	0.90[ASN][1000 genomes]
rs12204229	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204306	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12205335	0.90[ASN][1000 genomes]
rs12207470	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210493	0.90[ASN][1000 genomes]
rs12212554	0.90[ASN][1000 genomes]
rs12214000	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214369	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12214414	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215417	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216315	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169291	0.90[ASN][1000 genomes]
rs17516775	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs2024678	1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064502	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34059065	0.90[ASN][1000 genomes]
rs72986764	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72986775	0.90[ASN][1000 genomes]
rs9373254	0.82[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs9376479	1.00[ASN][1000 genomes]
rs9484322	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9495596	0.91[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];1.00[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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140227000-140247600	Weak transcription	Small Intestine	intestine
2	chr6:140238600-140242400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:140238600-140242400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:140239200-140242400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:140239800-140244800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:140239800-140246400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:140239800-140251600	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:140240000-140248000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:140240600-140242400	Enhancers	Brain Germinal Matrix	brain
10	chr6:140240800-140242400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:140240800-140242400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:140241200-140242400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:140241400-140242400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:140241400-140242600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:140241400-140247200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:140241600-140242400	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:140241600-140242400	Enhancers	Fetal Brain Male	brain
18	chr6:140241800-140247200	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:140241800-140247800	Weak transcription	Fetal Heart	heart
20	chr6:140242000-140242400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:140242200-140242800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr6:140242200-140246200	Weak transcription	Osteobl	bone
23	chr6:140242200-140247200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links