Variant report

Variant	rs4942995
Chromosome Location	chr13:51929304-51929305
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51928537..51930997-chr13:51935943..51937476,2	MCF-7	breast:
2	chr13:51928398..51929906-chr13:51933549..51935466,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269965	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs11148215	0.93[EUR][1000 genomes]
rs11148216	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11148217	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11148219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838784	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs11839165	0.93[EUR][1000 genomes]
rs11842573	0.93[EUR][1000 genomes]
rs11842878	0.93[EUR][1000 genomes]
rs11843638	0.93[EUR][1000 genomes]
rs11843641	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12100084	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100112	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184757	1.00[CEU][hapmap]
rs12584325	0.93[EUR][1000 genomes]
rs12584416	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12585171	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12585343	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12586110	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs1413103	0.93[EUR][1000 genomes]
rs1547710	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1570549	0.85[EUR][1000 genomes]
rs1570550	0.85[EUR][1000 genomes]
rs17194921	0.93[EUR][1000 genomes]
rs17194928	0.93[EUR][1000 genomes]
rs17194935	0.93[EUR][1000 genomes]
rs17194955	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17194985	0.93[EUR][1000 genomes]
rs17195027	0.93[EUR][1000 genomes]
rs17252180	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs17252193	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17252200	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs17529985	0.86[EUR][1000 genomes]
rs17790799	0.93[EUR][1000 genomes]
rs17790811	1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17790838	0.93[EUR][1000 genomes]
rs17837214	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs17837215	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17837216	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17837217	0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs4941699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4942993	0.89[EUR][1000 genomes]
rs4942994	0.89[EUR][1000 genomes]
rs4942996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942997	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4942998	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4942999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59024783	0.93[EUR][1000 genomes]
rs59215783	0.85[EUR][1000 genomes]
rs60860538	0.85[EUR][1000 genomes]
rs61956888	0.85[EUR][1000 genomes]
rs61956889	0.85[EUR][1000 genomes]
rs61956909	0.93[EUR][1000 genomes]
rs61956910	0.93[EUR][1000 genomes]
rs61956911	0.86[EUR][1000 genomes]
rs61956912	0.93[EUR][1000 genomes]
rs61956913	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs61956914	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs61956915	0.93[EUR][1000 genomes]
rs61956916	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs61956917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61956937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61956938	0.93[EUR][1000 genomes]
rs61956942	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61956943	0.93[EUR][1000 genomes]
rs61956944	0.93[EUR][1000 genomes]
rs61956945	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61956947	0.93[EUR][1000 genomes]
rs61956949	0.93[EUR][1000 genomes]
rs61956950	0.93[EUR][1000 genomes]
rs61956951	0.93[EUR][1000 genomes]
rs61956952	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61956955	0.93[EUR][1000 genomes]
rs73195977	0.93[EUR][1000 genomes]
rs73195982	0.93[EUR][1000 genomes]
rs73195996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73197808	0.93[EUR][1000 genomes]
rs7333988	0.84[CHD][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7338174	0.83[TSI][hapmap]
rs7400061	0.93[EUR][1000 genomes]
rs7984158	0.86[CHB][hapmap]
rs7988157	1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7990114	0.93[EUR][1000 genomes]
rs7992891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995268	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs8000429	0.88[CHB][hapmap]
rs8000433	0.86[CHB][hapmap]
rs8001625	0.85[EUR][1000 genomes]
rs8002112	0.89[CHB][hapmap]
rs9316535	0.93[EUR][1000 genomes]
rs9316537	0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9563041	0.93[EUR][1000 genomes]
rs9563042	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9563043	0.93[EUR][1000 genomes]
rs9563044	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9563045	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9563047	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9563049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9563050	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9563052	0.93[EUR][1000 genomes]
rs9563053	0.93[EUR][1000 genomes]
rs9563054	0.93[EUR][1000 genomes]
rs9563055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563056	0.86[EUR][1000 genomes]
rs9568564	0.85[EUR][1000 genomes]
rs9568565	0.85[EUR][1000 genomes]
rs9568566	0.93[EUR][1000 genomes]
rs9568567	0.93[EUR][1000 genomes]
rs9568568	0.93[EUR][1000 genomes]
rs9568569	0.93[EUR][1000 genomes]
rs9568570	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9568571	0.93[EUR][1000 genomes]
rs9568572	0.93[EUR][1000 genomes]
rs9568573	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9568574	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9568575	1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9568576	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9568578	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9568579	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9568580	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568581	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9568585	0.93[EUR][1000 genomes]
rs9568586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568588	0.93[EUR][1000 genomes]
rs9568589	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9568590	0.93[EUR][1000 genomes]
rs9568591	0.93[EUR][1000 genomes]
rs9568592	0.93[EUR][1000 genomes]
rs9568593	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9568594	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568596	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568609	0.86[EUR][1000 genomes]
rs9634684	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9634685	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs9634838	0.93[EUR][1000 genomes]
rs9634839	0.93[EUR][1000 genomes]
rs9634840	0.93[EUR][1000 genomes]
rs9634844	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4942995	Hs.123474	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51900400-51938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr13:51906000-51944400	Weak transcription	Spleen	Spleen
3	chr13:51906200-51935400	Weak transcription	HSMMtube	muscle
4	chr13:51907800-51933200	Weak transcription	Primary T cells from cord blood	blood
5	chr13:51911800-51938600	Weak transcription	Pancreas	Pancrea
6	chr13:51913400-51944600	Weak transcription	Aorta	Aorta
7	chr13:51915200-51929400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr13:51915400-51934000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:51916800-51931600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr13:51917200-51933600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:51917600-51933000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr13:51917600-51943200	Weak transcription	NHLF	lung
13	chr13:51917800-51942400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:51918200-51933200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:51918400-51938600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:51918600-51935600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr13:51918600-51945000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:51919000-51944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr13:51920200-51935800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:51921400-51935400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr13:51921400-51938400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:51921400-51938800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:51922400-51936600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:51922800-51941200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr13:51924000-51936200	Weak transcription	HUVEC	blood vessel
26	chr13:51924400-51934000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:51924400-51934400	Weak transcription	Adipose Nuclei	Adipose
28	chr13:51924400-51938600	Weak transcription	A549	lung
29	chr13:51924800-51936600	Weak transcription	Primary B cells from cord blood	blood
30	chr13:51925600-51935200	Weak transcription	Liver	Liver
31	chr13:51925800-51936400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr13:51927000-51934600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr13:51927800-51931600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr13:51927800-51933000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:51927800-51933200	Weak transcription	HSMM	muscle
36	chr13:51927800-51934200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr13:51927800-51935400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr13:51927800-51936400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:51927800-51937200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr13:51928000-51932000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr13:51928800-51933800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:51929000-51929400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr13:51929200-51930600	Enhancers	HepG2	liver

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