Variant report

Variant	rs12198294
Chromosome Location	chr6:38524025-38524026
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	chr6:38517461..38519604-chr6:38521981..38524241,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10484856	0.92[CEU][hapmap]
rs1073900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154188	0.88[CEU][hapmap]
rs12193868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199427	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12206218	0.92[CEU][hapmap]
rs12206371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208087	0.92[CEU][hapmap]
rs1406841	0.92[CEU][hapmap]
rs1590165	0.83[YRI][hapmap]
rs17543429	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2748156	0.81[CEU][hapmap]
rs2748173	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814887	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814890	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4254983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55869483	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083119	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56250767	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458060	0.80[CEU][hapmap]
rs6903004	0.92[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6924443	0.81[CEU][hapmap]
rs6927145	0.85[CEU][hapmap]
rs72853429	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7743871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752239	0.88[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7755619	0.87[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7761154	0.81[CEU][hapmap]
rs7767041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769475	0.82[YRI][hapmap]

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	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
2	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
3	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

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38494400-38524200	Weak transcription	Aorta	Aorta
2	chr6:38496600-38539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:38497000-38538800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:38497000-38539400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr6:38510600-38546800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:38513000-38539200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:38514200-38539400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:38515600-38535800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:38516000-38538800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:38517800-38535000	Weak transcription	Brain Substantia Nigra	brain
11	chr6:38519200-38538800	Weak transcription	Primary T cells from cord blood	blood
12	chr6:38519200-38539400	Weak transcription	Left Ventricle	heart
13	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:38521400-38532000	Weak transcription	Primary B cells from cord blood	blood
15	chr6:38522000-38524200	Enhancers	Fetal Brain Female	brain
16	chr6:38522000-38524800	Enhancers	Fetal Brain Male	brain
17	chr6:38522800-38534800	Weak transcription	Fetal Heart	heart
18	chr6:38522800-38535200	Weak transcription	Psoas Muscle	Psoas
19	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
20	chr6:38523200-38534800	Weak transcription	NHLF	lung
21	chr6:38524000-38537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:38524000-38539200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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