Variant report

Variant	rs12640392
Chromosome Location	chr4:87198203-87198204
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	chr4:87195749..87198427-chr4:87210790..87213318,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10003556	0.82[ASN][1000 genomes]
rs10003756	0.84[ASN][1000 genomes]
rs10004539	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10010011	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10016847	0.82[ASN][1000 genomes]
rs10022904	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs10026060	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs10026338	0.84[ASN][1000 genomes]
rs10029339	0.85[JPT][hapmap]
rs10034428	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10035072	0.85[CHB][hapmap]
rs10213302	0.89[ASN][1000 genomes]
rs10213451	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10213453	0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10516769	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1108429	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs11097101	0.89[ASN][1000 genomes]
rs11097102	0.85[JPT][hapmap]
rs11097103	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12650052	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1460758	0.85[JPT][hapmap]
rs1460759	0.85[JPT][hapmap]
rs1460760	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1460761	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1460763	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1460764	0.82[ASN][1000 genomes]
rs1599313	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1599314	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17011421	0.82[ASN][1000 genomes]
rs17011460	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17011540	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs17011547	0.85[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs17011564	0.85[JPT][hapmap]
rs17011584	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs17011588	0.84[ASN][1000 genomes]
rs17011592	0.85[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17011654	1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17011655	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17418062	0.85[CHB][hapmap]
rs1903360	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1903361	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs2035056	0.82[ASN][1000 genomes]
rs2035058	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2199308	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2199309	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs28425193	0.84[ASN][1000 genomes]
rs28583812	0.84[ASN][1000 genomes]
rs28642002	0.89[ASN][1000 genomes]
rs2869421	0.83[JPT][hapmap]
rs2869422	0.84[ASN][1000 genomes]
rs28722990	0.84[ASN][1000 genomes]
rs28791572	0.85[ASN][1000 genomes]
rs28803851	0.87[ASN][1000 genomes]
rs28830922	0.87[ASN][1000 genomes]
rs28839895	0.89[ASN][1000 genomes]
rs28870188	0.84[ASN][1000 genomes]
rs28896887	0.89[ASN][1000 genomes]
rs2904090	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4132490	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4561895	0.89[ASN][1000 genomes]
rs59124829	0.89[ASN][1000 genomes]
rs6531906	0.85[JPT][hapmap]
rs6531907	0.85[JPT][hapmap]
rs6531909	0.85[JPT][hapmap]
rs6531910	0.83[JPT][hapmap]
rs6531911	0.85[JPT][hapmap]
rs67768527	0.84[ASN][1000 genomes]
rs6817452	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6821819	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6826951	0.82[ASN][1000 genomes]
rs6827698	0.85[JPT][hapmap]
rs6828947	0.85[JPT][hapmap]
rs6829870	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6832259	0.84[JPT][hapmap]
rs6844363	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6844365	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6845605	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs6845742	0.82[ASN][1000 genomes]
rs7440491	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7655797	0.82[ASN][1000 genomes]
rs7663388	0.89[ASN][1000 genomes]
rs7663763	0.89[ASN][1000 genomes]
rs7669487	0.82[ASN][1000 genomes]
rs7678480	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7680934	0.85[JPT][hapmap]
rs7685419	0.84[ASN][1000 genomes]
rs7685683	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7687771	0.84[JPT][hapmap]
rs7695707	0.89[ASN][1000 genomes]
rs7699047	0.82[ASN][1000 genomes]
rs9307016	0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs9654155	0.81[ASN][1000 genomes]
rs9884127	0.85[JPT][hapmap]
rs9994303	0.84[ASN][1000 genomes]
rs9996693	0.82[ASN][1000 genomes]
rs9997633	0.85[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9999403	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv934210	chr4:87197339-87325578	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS 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	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12640392	OK	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87188800-87201600	Weak transcription	Brain Anterior Caudate	brain
2	chr4:87190800-87199400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:87194000-87205400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:87196200-87200400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:87196200-87204400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:87196400-87200600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:87197400-87201000	Enhancers	Brain Angular Gyrus	brain
8	chr4:87197600-87199600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr4:87197800-87198400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:87197800-87198400	Enhancers	Brain Germinal Matrix	brain
11	chr4:87197800-87198400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:87198000-87198400	Enhancers	Brain Hippocampus Middle	brain
13	chr4:87198000-87201800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:87198200-87199600	Enhancers	Adipose Nuclei	Adipose
15	chr4:87198200-87200600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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