Variant report

Variant	rs41477846
Chromosome Location	chr4:86644130-86644131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10017047	0.93[CEU][hapmap]
rs10033273	0.93[CEU][hapmap]
rs1020584	1.00[CEU][hapmap]
rs1031987	0.99[ASN][1000 genomes]
rs11097072	0.80[AMR][1000 genomes]
rs11097073	0.80[AMR][1000 genomes]
rs11722392	0.93[ASN][1000 genomes]
rs11731040	0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs11735639	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs12054628	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs12644984	0.95[ASN][1000 genomes]
rs12646641	0.84[ASN][1000 genomes]
rs12647014	0.89[ASN][1000 genomes]
rs12648692	0.80[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12650494	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs13112493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13128115	0.93[CEU][hapmap];0.95[MEX][hapmap]
rs13146939	0.92[CEU][hapmap]
rs13152150	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs1482091	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs1482092	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1482095	0.96[ASN][1000 genomes]
rs17010599	0.82[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs17010632	0.93[CEU][hapmap]
rs17010697	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1871864	0.93[CEU][hapmap]
rs1871865	0.93[CEU][hapmap]
rs2624023	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343848	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs343852	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3889735	0.82[CHB][hapmap]
rs4413396	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs4455406	0.92[ASN][1000 genomes]
rs56989679	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57065351	0.89[ASN][1000 genomes]
rs6531862	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531863	0.93[ASN][1000 genomes]
rs6819529	0.84[EUR][1000 genomes]
rs6831420	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs6839040	0.95[ASN][1000 genomes]
rs6853196	0.96[ASN][1000 genomes]
rs6855390	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72656252	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72656285	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72656294	0.82[AMR][1000 genomes]
rs7439720	0.93[CEU][hapmap]
rs7661884	0.93[ASN][1000 genomes]
rs7674888	1.00[CEU][hapmap];0.80[AMR][1000 genomes]
rs7675688	0.88[ASN][1000 genomes]
rs7677064	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs7680588	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs7682971	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs7685320	0.95[ASN][1000 genomes]
rs7697134	0.98[ASN][1000 genomes]
rs931195	0.93[CEU][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv829999	chr4:86500257-86666019	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
6	esv274900	chr4:86643742-86644130	Weak transcription Strong transcription Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86632000-86647000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:86633600-86644800	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:86638000-86646600	Weak transcription	Small Intestine	intestine
4	chr4:86638200-86646600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:86639000-86644800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr4:86639400-86645400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:86639400-86646800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:86639600-86645400	Weak transcription	NHLF	lung
9	chr4:86639600-86646200	Weak transcription	Fetal Lung	lung
10	chr4:86641400-86644400	Enhancers	HSMM	muscle
11	chr4:86641600-86644400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:86641600-86646800	Weak transcription	Ovary	ovary
13	chr4:86642000-86645400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:86642000-86646400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:86642000-86646600	Weak transcription	Osteobl	bone
16	chr4:86642200-86646600	Weak transcription	Fetal Heart	heart
17	chr4:86642400-86646800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:86642600-86646200	Weak transcription	Adipose Nuclei	Adipose
19	chr4:86642600-86646800	Weak transcription	Placenta	Placenta
20	chr4:86643000-86644400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:86643000-86645200	Strong transcription	Primary B cells from cord blood	blood
22	chr4:86643200-86646000	Weak transcription	A549	lung
23	chr4:86643200-86646600	Weak transcription	Pancreas	Pancrea
24	chr4:86643400-86644800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:86643400-86645400	Enhancers	HSMMtube	muscle
26	chr4:86643600-86644400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:86643600-86644600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:86643600-86644800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:86643600-86645000	Enhancers	Muscle Satellite Cultured Cells	--
30	chr4:86644000-86646000	Weak transcription	K562	blood
31	chr4:86644000-86650200	Enhancers	NHDF-Ad	bronchial

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