Variant report

Variant	rs12702390
Chromosome Location	chr7:47841059-47841060
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	chr7:47840087..47841589-chr7:47841820..47843943,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10231581	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10269813	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11760871	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12702385	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12702386	0.86[ASN][1000 genomes]
rs12702388	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12702389	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13240669	0.82[ASN][1000 genomes]
rs1551277	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2348459	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3926198	0.82[ASN][1000 genomes]
rs4724644	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5022192	0.82[ASN][1000 genomes]
rs6463447	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6463448	1.00[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs6943728	1.00[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs6962348	0.91[ASN][1000 genomes]
rs6963565	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6969522	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7801465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs965143	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs965144	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9719534	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9770658	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47817200-47846600	Weak transcription	Left Ventricle	heart
2	chr7:47823400-47847200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:47823400-47849400	Weak transcription	Psoas Muscle	Psoas
4	chr7:47823400-47852200	Weak transcription	Right Ventricle	heart
5	chr7:47826600-47844000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:47827000-47851400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:47827600-47842000	Weak transcription	Fetal Intestine Small	intestine
8	chr7:47827600-47844400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:47827600-47845800	Weak transcription	Fetal Stomach	stomach
10	chr7:47834400-47847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:47835400-47845800	Weak transcription	Colon Smooth Muscle	Colon
12	chr7:47836200-47843400	Weak transcription	A549	lung
13	chr7:47836200-47844400	Weak transcription	NH-A	brain
14	chr7:47836200-47844600	Weak transcription	Ovary	ovary
15	chr7:47836400-47844400	Weak transcription	NHLF	lung
16	chr7:47838400-47853600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr7:47838800-47847800	Enhancers	HepG2	liver
18	chr7:47839200-47841200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:47839200-47845800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:47839400-47843200	Weak transcription	HSMM	muscle
21	chr7:47840000-47842400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr7:47840200-47842000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr7:47840600-47841200	Enhancers	Esophagus	oesophagus
24	chr7:47840600-47841600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:47840600-47842200	Enhancers	HMEC	breast
26	chr7:47840800-47842200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:47840800-47847400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:47841000-47841400	Flanking Active TSS	NHEK	skin

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