Variant report

Variant	rs13204837
Chromosome Location	chr6:140283125-140283126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140281644..140284069-chr6:140292281..140294292,2	K562	blood:
2	chr6:140281089..140284069-chr6:140290932..140294292,3	K562	blood:
3	chr6:139695184..139697325-chr6:140282600..140285421,2	MCF-7	breast:
4	chr6:140282684..140285359-chr6:140286233..140287873,2	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1028469	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10434888	1.00[CEU][hapmap]
rs10872525	1.00[CEU][hapmap]
rs12175776	0.82[EUR][1000 genomes]
rs12525047	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12526885	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12663217	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12663483	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13191189	0.93[CEU][hapmap]
rs13194747	0.87[EUR][1000 genomes]
rs13194827	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1416289	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17069768	1.00[CEU][hapmap]
rs1933742	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1953788	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1953789	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586246	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs587235	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs592056	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs598498	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs616279	0.89[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs618515	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs622216	0.97[ASN][1000 genomes]
rs62429515	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62429516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62429517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs647968	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs648510	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs650774	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs67013338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679849	0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs680290	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs681235	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6926807	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928433	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724061	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743656	0.89[ASN][1000 genomes]
rs7758187	1.00[CEU][hapmap]
rs856646	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9373255	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9373256	1.00[CEU][hapmap]
rs9373259	1.00[CEU][hapmap]
rs9376482	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9376485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9376494	1.00[CEU][hapmap]
rs9385888	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385895	1.00[CEU][hapmap]
rs9385901	0.87[CEU][hapmap]
rs9385902	1.00[CEU][hapmap]
rs9389733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9389741	1.00[CEU][hapmap]
rs9399298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9399299	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399304	0.95[CEU][hapmap]
rs9399308	1.00[CEU][hapmap]
rs9403134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403135	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9403148	1.00[CEU][hapmap]
rs9495636	0.88[YRI][hapmap]
rs9495641	0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13204837	HECA	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140272400-140283800	Weak transcription	Fetal Heart	heart
2	chr6:140280000-140286600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:140281400-140283200	Enhancers	Colon Smooth Muscle	Colon
4	chr6:140281600-140284800	Enhancers	Liver	Liver
5	chr6:140282200-140283800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:140282200-140285800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:140282200-140286000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:140282200-140286400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:140282200-140288800	Weak transcription	NHDF-Ad	bronchial
10	chr6:140282400-140283600	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr6:140282400-140283800	Weak transcription	Fetal Lung	lung
12	chr6:140282600-140283600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:140282600-140284200	Weak transcription	Fetal Stomach	stomach
14	chr6:140282800-140283800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:140282800-140285800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:140282800-140285800	Weak transcription	Fetal Kidney	kidney

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