Variant report

Variant	rs346490
Chromosome Location	chr4:86874428-86874429
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	chr4:86855497..86859080-chr4:86873833..86876584,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs189395	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs189396	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2043647	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2136782	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164538	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2575681	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2575682	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589505	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589510	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2665869	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2665876	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346469	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346470	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346472	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346473	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346476	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs346477	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346482	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346483	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346487	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346491	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346495	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346496	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346499	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346500	0.83[EUR][1000 genomes]
rs346501	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62305515	0.89[ASN][1000 genomes]
rs62305516	0.89[ASN][1000 genomes]
rs62305518	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86851400-86874600	Weak transcription	HSMMtube	muscle
2	chr4:86851600-86874800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:86854000-86893000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr4:86854200-86880200	Weak transcription	Gastric	stomach
5	chr4:86854200-86893000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
7	chr4:86858800-86876600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:86860400-86874800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:86862400-86877200	Weak transcription	Liver	Liver
10	chr4:86863600-86902000	Weak transcription	Pancreas	Pancrea
11	chr4:86864000-86877000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:86872400-86875400	Enhancers	HUVEC	blood vessel
13	chr4:86872400-86875600	Strong transcription	Primary B cells from cord blood	blood
14	chr4:86873200-86875800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr4:86873200-86875800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:86873400-86874600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:86873400-86874800	Enhancers	A549	lung
18	chr4:86873400-86875000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr4:86873400-86875200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:86873400-86875400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:86873400-86875400	Enhancers	Osteobl	bone
22	chr4:86873400-86875600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:86873400-86875800	Enhancers	HSMM	muscle
24	chr4:86873600-86875000	Enhancers	NH-A	brain
25	chr4:86873600-86875000	Enhancers	NHLF	lung
26	chr4:86873600-86875200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:86873600-86875200	Enhancers	Adipose Nuclei	Adipose
28	chr4:86873600-86875400	Enhancers	HMEC	breast
29	chr4:86873800-86875000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:86874000-86875000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr4:86874000-86876400	Weak transcription	Fetal Kidney	kidney
32	chr4:86874200-86874600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr4:86874200-86875000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr4:86874200-86875000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:86874200-86875000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:86874200-86875000	Enhancers	Ovary	ovary
37	chr4:86874200-86875000	Enhancers	Right Atrium	heart
38	chr4:86874200-86875200	Enhancers	H1 Cell Line	embryonic stem cell
39	chr4:86874200-86875200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:86874200-86875200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:86874200-86875200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:86874200-86875200	Enhancers	GM12878-XiMat	blood
43	chr4:86874200-86875400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr4:86874200-86875400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr4:86874200-86875400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr4:86874200-86875600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr4:86874200-86875800	Enhancers	Fetal Muscle Leg	muscle
48	chr4:86874400-86874800	Weak transcription	Fetal Stomach	stomach
49	chr4:86874400-86875200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr4:86874400-86875600	Enhancers	NHDF-Ad	bronchial

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