Variant report

Variant	rs958800
Chromosome Location	chr4:86714299-86714300
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	chr4:86713042..86715039-chr4:87371799..87373395,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10020335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120399	0.80[EUR][1000 genomes]
rs13127292	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149705	1.00[JPT][hapmap]
rs1452676	1.00[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs1452683	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17399388	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982429	0.87[EUR][1000 genomes]
rs1982430	0.87[EUR][1000 genomes]
rs28375213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28522299	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28544562	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28841671	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3028238	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62315355	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62315356	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62315357	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670874	0.89[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs9307010	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879517	chr4:86677107-86739805	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs958800	LIN54	cis	cerebellum	SCAN
rs958800	C4orf36	cis	parietal	SCAN
rs958800	FAM13A	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86701000-86728800	Weak transcription	Right Ventricle	heart
2	chr4:86701200-86715600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:86704000-86715600	Enhancers	Osteobl	bone
4	chr4:86704000-86719800	Enhancers	NHDF-Ad	bronchial
5	chr4:86705800-86719600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:86708400-86718200	Weak transcription	Aorta	Aorta
7	chr4:86709000-86714400	Weak transcription	NH-A	brain
8	chr4:86709000-86727000	Weak transcription	HSMMtube	muscle
9	chr4:86709200-86727000	Weak transcription	HSMM	muscle
10	chr4:86711000-86719800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:86711200-86715600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:86711600-86715200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:86712400-86718000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:86712600-86714400	Enhancers	Fetal Kidney	kidney
15	chr4:86712800-86715200	Enhancers	Adipose Nuclei	Adipose
16	chr4:86712800-86715800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:86712800-86719400	Weak transcription	Right Atrium	heart
18	chr4:86713000-86714800	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr4:86713000-86718000	Weak transcription	Left Ventricle	heart
20	chr4:86713200-86717800	Weak transcription	Primary B cells from cord blood	blood
21	chr4:86713200-86717800	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:86713200-86718000	Weak transcription	Fetal Stomach	stomach
23	chr4:86713200-86726400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:86713400-86715200	Enhancers	Fetal Lung	lung
25	chr4:86713600-86714800	Enhancers	Colon Smooth Muscle	Colon
26	chr4:86713600-86715400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:86713800-86714400	Enhancers	NHLF	lung
28	chr4:86713800-86714800	Enhancers	Rectal Smooth Muscle	rectum
29	chr4:86714000-86714600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:86714000-86714600	Flanking Active TSS	HUVEC	blood vessel
31	chr4:86714000-86714800	Enhancers	Fetal Heart	heart
32	chr4:86714200-86714400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:86714200-86714800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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