Variant report

Variant	rs744556
Chromosome Location	chr2:190351066-190351067
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	chr2:190347309..190351333-chr2:190419513..190421740,3	MCF-7	breast:
2	chr2:190349773..190352043-chr2:190405227..190407420,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10166420	0.93[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs10198663	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs10497700	0.82[AFR][1000 genomes]
rs1157910	0.89[LWK][hapmap];0.80[AFR][1000 genomes]
rs11678414	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12613876	0.84[AFR][1000 genomes]
rs12613903	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12622720	0.93[ASN][1000 genomes]
rs12623394	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693539	0.87[ASN][1000 genomes]
rs12693540	0.93[ASN][1000 genomes]
rs12987962	0.84[AFR][1000 genomes]
rs13009912	0.93[ASN][1000 genomes]
rs13010531	0.80[AFR][1000 genomes]
rs13015203	0.81[AFR][1000 genomes]
rs13015207	0.87[ASN][1000 genomes]
rs13018252	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs13032853	0.91[LWK][hapmap];0.80[AFR][1000 genomes]
rs1356976	0.80[ASN][1000 genomes]
rs1520854	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs1520856	0.80[ASN][1000 genomes]
rs1520857	0.86[LWK][hapmap]
rs1520858	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1520866	0.91[ASN][1000 genomes]
rs1595749	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs16831454	0.91[ASN][1000 genomes]
rs1851104	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.82[ASN][1000 genomes]
rs1866605	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs1898971	0.93[ASN][1000 genomes]
rs1992295	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs2304702	0.89[ASN][1000 genomes]
rs2304703	0.80[AFR][1000 genomes]
rs2351934	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4309611	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4666775	0.91[ASN][1000 genomes]
rs4667281	0.89[LWK][hapmap];0.80[AFR][1000 genomes]
rs4667284	0.94[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6434339	0.81[JPT][hapmap]
rs6434342	0.84[ASN][1000 genomes]
rs6434343	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs6738193	0.87[ASN][1000 genomes]
rs6747222	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs734859	0.93[ASN][1000 genomes]
rs745742	0.93[ASN][1000 genomes]
rs7574403	0.87[ASN][1000 genomes]
rs7576165	0.81[JPT][hapmap]
rs8179541	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs893407	0.93[ASN][1000 genomes]
rs893408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963738	0.80[AFR][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs744556	AC013439.4	cis	Muscle Skeletal	GTEx
rs744556	PMS1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190351800	Weak transcription	Psoas Muscle	Psoas
2	chr2:190335000-190366200	Weak transcription	Ovary	ovary
3	chr2:190335800-190352600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:190339600-190352600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:190340800-190352400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:190341800-190351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:190342400-190357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:190349200-190365000	Weak transcription	Fetal Intestine Large	intestine
9	chr2:190349600-190351400	Enhancers	HSMMtube	muscle
10	chr2:190349600-190351600	Weak transcription	Placenta	Placenta
11	chr2:190350000-190351600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:190350000-190352200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:190350800-190353000	Enhancers	Liver	Liver
14	chr2:190351000-190351400	Enhancers	HMEC	breast
15	chr2:190351000-190351800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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