Variant report

Variant	rs10420746
Chromosome Location	chr19:38274465-38274466
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	chr19:38269026..38272405-chr19:38273458..38276244,3	K562	blood:
2	chr19:38145236..38146842-chr19:38274136..38275827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120784	Chromatin interaction
ENSG00000189144	Chromatin interaction
ENSG00000267422	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10048511	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10403173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10404567	1.00[CEU][hapmap]
rs10409402	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10409487	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10415548	0.83[CEU][hapmap]
rs11083432	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs1119229	0.88[CEU][hapmap]
rs11673023	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12974225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12979640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1643466	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1643467	1.00[CEU][hapmap]
rs1643468	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs16958861	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16958863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs171376	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1725481	1.00[CEU][hapmap]
rs1725482	1.00[CEU][hapmap]
rs1725499	0.83[CEU][hapmap]
rs1974714	0.87[ASN][1000 genomes]
rs1975937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2075281	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2287229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs241932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs241933	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs241950	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2909088	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2909093	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2909098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2909100	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2909102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2909105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2909109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2927739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2927740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2927747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972434	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2972437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972445	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2972448	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3095726	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112434	0.81[EUR][1000 genomes]
rs353410	0.83[CEU][hapmap]
rs353411	0.83[CEU][hapmap]
rs353414	1.00[CEU][hapmap]
rs353415	1.00[CEU][hapmap]
rs353423	1.00[CEU][hapmap]
rs3786869	0.83[CEU][hapmap]
rs3829688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4239516	0.83[CEU][hapmap]
rs4802135	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4803509	0.90[ASN][1000 genomes]
rs4803524	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs4803551	0.88[CEU][hapmap]
rs4803573	0.88[CEU][hapmap]
rs6508742	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs705491	0.88[CEU][hapmap]
rs705492	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs705493	0.88[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs705495	0.88[CEU][hapmap]
rs7250409	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs8102579	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs8103633	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs8112706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8113521	0.83[CEU][hapmap]
rs833895	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs833914	0.80[CEU][hapmap]
rs833926	1.00[CEU][hapmap]
rs856300	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs856304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304569	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs958305	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs968073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv960835	chr19:38270238-38293706	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38270800-38276400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:38270800-38277600	Weak transcription	Ovary	ovary
3	chr19:38270800-38277800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38270800-38279800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:38270800-38281000	Weak transcription	Right Ventricle	heart
6	chr19:38270800-38281400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:38271000-38275200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr19:38271000-38281000	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:38271200-38274600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr19:38271400-38275400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:38271400-38276600	Weak transcription	Fetal Lung	lung
12	chr19:38271400-38281000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr19:38272600-38277800	Weak transcription	Left Ventricle	heart
14	chr19:38274200-38278000	ZNF genes & repeats	Liver	Liver

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