Variant report

Variant	rs1005995
Chromosome Location	chr6:39261244-39261245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39192543..39195270-chr6:39259985..39261560,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1182864	0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs12191604	0.82[ASN][1000 genomes]
rs12191756	0.81[ASN][1000 genomes]
rs2253582	0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2395719	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2395720	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2758864	0.82[ASN][1000 genomes]
rs2758865	0.81[ASN][1000 genomes]
rs2758866	0.82[ASN][1000 genomes]
rs2758867	0.82[ASN][1000 genomes]
rs2758868	0.80[ASN][1000 genomes]
rs2758869	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2758871	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2758872	0.85[ASN][1000 genomes]
rs2758874	0.95[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2758906	0.87[ASN][1000 genomes]
rs2758909	0.85[ASN][1000 genomes]
rs2758912	0.88[GIH][hapmap]
rs2815019	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2815020	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2815024	0.82[ASN][1000 genomes]
rs2815025	0.81[ASN][1000 genomes]
rs2815026	0.82[ASN][1000 genomes]
rs2815027	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2815028	0.82[ASN][1000 genomes]
rs2815029	0.82[ASN][1000 genomes]
rs2815030	0.85[ASN][1000 genomes]
rs2815031	0.82[ASN][1000 genomes]
rs2815032	0.82[ASN][1000 genomes]
rs2815035	0.82[ASN][1000 genomes]
rs2815036	0.82[ASN][1000 genomes]
rs2815037	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2815038	0.82[ASN][1000 genomes]
rs2815039	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2815040	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2815041	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2815042	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2815044	0.85[ASN][1000 genomes]
rs2815045	0.81[ASN][1000 genomes]
rs2815061	0.99[ASN][1000 genomes]
rs2815064	0.86[ASN][1000 genomes]
rs2815066	0.85[ASN][1000 genomes]
rs4714233	1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs731419	0.86[ASN][1000 genomes]
rs7746595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9394580	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS 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 target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1005995	LOC221442	cis	parietal	SCAN
rs1005995	TBCC	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39248400-39263400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:39248400-39263400	Weak transcription	Right Atrium	heart
3	chr6:39257800-39265800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr6:39258000-39265600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:39258600-39262000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:39260000-39261400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
7	chr6:39260200-39261600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:39260800-39263200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:39260800-39263200	Weak transcription	Ovary	ovary
10	chr6:39261000-39261400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:39261000-39261800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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