Variant report

Variant	rs4896582
Chromosome Location	chr6:142703877-142703878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142697707..142700330-chr6:142702224..142704168,2	MCF-7	breast:
2	chr6:142615209..142616975-chr6:142701989..142704328,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1040525	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs1040526	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1342060	0.83[EUR][1000 genomes]
rs1360194	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs1418201	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1891308	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2039986	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs2039987	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2050157	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2294764	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs2294771	0.89[EUR][1000 genomes]
rs262115	0.85[EUR][1000 genomes]
rs3748069	0.89[EUR][1000 genomes]
rs3817929	0.89[EUR][1000 genomes]
rs6570507	0.88[CEU][hapmap];0.96[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6570508	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570509	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs6570510	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs6909857	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs6929442	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs6937121	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7741741	0.87[EUR][1000 genomes]
rs7753012	0.89[CEU][hapmap];0.89[CHB][hapmap]
rs7754638	0.89[EUR][1000 genomes]
rs7755109	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs7756305	0.84[EUR][1000 genomes]
rs7763064	0.84[EUR][1000 genomes]
rs7770386	0.87[EUR][1000 genomes]
rs7774095	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs7776375	0.87[EUR][1000 genomes]
rs9373346	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs9389984	0.82[EUR][1000 genomes]
rs9389985	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs9389986	0.89[CEU][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9389987	0.85[EUR][1000 genomes]
rs9399401	0.83[EUR][1000 genomes]
rs9403380	0.86[EUR][1000 genomes]
rs9403381	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs9403382	0.89[EUR][1000 genomes]
rs9403383	0.82[CEU][hapmap];0.92[EUR][1000 genomes]
rs9403387	0.88[EUR][1000 genomes]
rs9496346	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs9496369	0.91[EUR][1000 genomes]
rs9496374	0.90[EUR][1000 genomes]
rs9496392	0.84[EUR][1000 genomes]
rs962554	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs972982	0.89[EUR][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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv970353	chr6:142702492-142705790	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	18391950	GWAS catalog

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142698600-142706200	Weak transcription	NHLF	lung
2	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:142698800-142707600	Weak transcription	Placenta	Placenta
4	chr6:142698800-142707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:142699600-142708000	Weak transcription	Pancreas	Pancrea
6	chr6:142699600-142709200	Weak transcription	Fetal Intestine Large	intestine
7	chr6:142699800-142705400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:142699800-142708000	Weak transcription	Liver	Liver
9	chr6:142699800-142709000	Weak transcription	Fetal Intestine Small	intestine
10	chr6:142699800-142718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:142699800-142719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:142700000-142705600	Weak transcription	NHEK	skin
13	chr6:142700000-142705800	Weak transcription	NH-A	brain
14	chr6:142700000-142706000	Weak transcription	HSMMtube	muscle
15	chr6:142700000-142714200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:142700200-142705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:142700400-142705600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:142700400-142709000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:142700400-142709000	Weak transcription	Fetal Lung	lung
20	chr6:142700600-142705800	Weak transcription	Hela-S3	cervix
21	chr6:142702200-142704400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:142702200-142707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:142702600-142706000	Strong transcription	HepG2	liver
24	chr6:142702800-142705000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr6:142702800-142705800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:142703200-142704000	Enhancers	NHDF-Ad	bronchial
27	chr6:142703200-142704400	Weak transcription	HSMM	muscle
28	chr6:142703200-142708200	Strong transcription	HUVEC	blood vessel
29	chr6:142703400-142705600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:142703400-142705800	Enhancers	A549	lung
31	chr6:142703600-142704800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:142703600-142705600	Weak transcription	Osteobl	bone
33	chr6:142703800-142704000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:142703800-142707400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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