Variant report

Variant	rs3897941
Chromosome Location	chr7:40272081-40272082
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:40271921..40272777-chr7:40766227..40766815,2	MCF-7	breast:
2	chr7:40271902..40272542-chr7:40644343..40645096,2	MCF-7	breast:
3	chr7:40271945..40272762-chr7:40522914..40523878,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10226951	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10247300	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs10248078	0.85[ASN][1000 genomes]
rs10251283	0.82[JPT][hapmap]
rs10252609	0.84[ASN][1000 genomes]
rs10258258	0.82[JPT][hapmap]
rs10261911	0.85[ASN][1000 genomes]
rs10262201	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs10270438	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs10282170	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10951628	0.86[ASN][1000 genomes]
rs11762020	0.89[ASN][1000 genomes]
rs11763124	0.83[ASN][1000 genomes]
rs12668394	0.85[ASN][1000 genomes]
rs12701807	0.88[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12701810	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12701812	0.82[JPT][hapmap]
rs13227773	0.84[JPT][hapmap]
rs13235423	0.84[ASN][1000 genomes]
rs13235432	0.84[ASN][1000 genomes]
rs13244588	0.85[ASN][1000 genomes]
rs13247751	0.85[ASN][1000 genomes]
rs13247974	0.85[ASN][1000 genomes]
rs2329771	0.83[ASN][1000 genomes]
rs34830114	0.87[ASN][1000 genomes]
rs4129802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4129803	0.80[CHB][hapmap]
rs4585651	0.84[ASN][1000 genomes]
rs4637704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4720355	0.86[ASN][1000 genomes]
rs4723935	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4723936	0.87[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4723946	0.82[JPT][hapmap]
rs55648745	0.85[ASN][1000 genomes]
rs57205249	0.89[ASN][1000 genomes]
rs58664838	0.89[ASN][1000 genomes]
rs61003774	0.89[ASN][1000 genomes]
rs6462967	0.80[CHB][hapmap]
rs6462970	0.82[JPT][hapmap]
rs67382823	0.89[ASN][1000 genomes]
rs6944348	0.82[ASN][1000 genomes]
rs6946123	0.85[ASN][1000 genomes]
rs6946980	0.80[CHB][hapmap]
rs6955478	0.88[ASN][1000 genomes]
rs6956802	0.88[ASN][1000 genomes]
rs6961025	0.86[ASN][1000 genomes]
rs6961151	0.86[ASN][1000 genomes]
rs6962341	0.82[JPT][hapmap]
rs6963317	0.85[ASN][1000 genomes]
rs6964864	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6967242	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6969419	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6979118	0.82[JPT][hapmap]
rs73131776	0.89[ASN][1000 genomes]
rs756328	0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7778070	0.83[ASN][1000 genomes]
rs7800400	0.83[ASN][1000 genomes]
rs7802836	0.82[JPT][hapmap]
rs952750	0.80[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032278	chr7:40097371-40396300	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv464438	chr7:40193535-40350887	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv606710	chr7:40193535-40350887	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1019032	chr7:40204606-40280323	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv887983	chr7:40211563-40284166	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv606711	chr7:40225129-40360257	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv887984	chr7:40227307-40284166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv887985	chr7:40265510-40586674	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40258800-40273800	Weak transcription	Fetal Intestine Small	intestine
2	chr7:40269400-40272600	Enhancers	Fetal Heart	heart
3	chr7:40271600-40272200	Enhancers	HSMM	muscle
4	chr7:40271800-40272200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr7:40271800-40272200	Enhancers	Fetal Intestine Large	intestine
6	chr7:40271800-40272200	Enhancers	Hela-S3	cervix
7	chr7:40271800-40272200	Enhancers	HSMMtube	muscle
8	chr7:40271800-40272400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:40271800-40272600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr7:40272000-40272200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:40272000-40272200	Enhancers	Liver	Liver
12	chr7:40272000-40272200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr7:40272000-40272600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:40272000-40272600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:40272000-40272600	Enhancers	NH-A	brain

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