Variant report

Variant	rs4839780
Chromosome Location	chr6:100909398-100909399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:100906855..100909524-chr6:100935004..100937170,2	MCF-7	breast:
2	chr6:100907831..100909801-chr6:100918117..100920075,2	MCF-7	breast:
3	chr6:100908327..100910621-chr6:100914553..100916127,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10457800	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11155472	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11155477	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12208241	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12212939	0.87[EUR][1000 genomes]
rs12664707	0.87[EUR][1000 genomes]
rs13201976	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1894561	0.82[EUR][1000 genomes]
rs2007134	0.84[EUR][1000 genomes]
rs2071826	0.82[EUR][1000 genomes]
rs2157342	0.87[EUR][1000 genomes]
rs2213594	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2213595	0.82[EUR][1000 genomes]
rs2397974	0.84[EUR][1000 genomes]
rs241819	0.81[CEU][hapmap];0.90[EUR][1000 genomes]
rs3798491	0.82[EUR][1000 genomes]
rs4840132	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs4840133	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6901854	0.84[EUR][1000 genomes]
rs6903206	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6910391	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6929748	0.82[EUR][1000 genomes]
rs6939998	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7748269	0.82[EUR][1000 genomes]
rs7751185	0.81[EUR][1000 genomes]
rs7751526	0.81[EUR][1000 genomes]
rs7773043	0.87[EUR][1000 genomes]
rs7773661	0.87[EUR][1000 genomes]
rs9373504	0.82[EUR][1000 genomes]
rs9386154	0.84[EUR][1000 genomes]

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	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS 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	nsv1028122	chr6:100774245-100964347	Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv515895	chr6:100868779-100910798	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
6	nsv533053	chr6:100883636-100911512	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100902000-100913600	Active TSS	Psoas Muscle	Psoas
2	chr6:100906600-100914200	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr6:100906800-100914400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:100906800-100914600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:100907200-100909400	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr6:100907400-100913600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:100908000-100913600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:100908000-100913800	Bivalent/Poised TSS	NHDF-Ad	bronchial
9	chr6:100908000-100914800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:100908200-100911000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:100908400-100909400	Enhancers	Dnd41	blood
12	chr6:100908400-100911200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
13	chr6:100908400-100913800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:100908600-100909400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:100908600-100909400	Active TSS	Pancreas	Pancrea
16	chr6:100908600-100909600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr6:100908600-100909600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:100908600-100909600	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
19	chr6:100908600-100910600	Active TSS	A549	lung
20	chr6:100908600-100913400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:100908600-100913400	Active TSS	HSMM	muscle
22	chr6:100908600-100913600	Active TSS	HSMMtube	muscle
23	chr6:100908800-100909400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr6:100908800-100909400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:100908800-100909600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:100908800-100909600	Enhancers	Right Ventricle	heart
27	chr6:100908800-100909800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr6:100908800-100910000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:100908800-100910000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
30	chr6:100908800-100910400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:100908800-100911800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
32	chr6:100908800-100914000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr6:100909000-100909400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:100909000-100909400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
35	chr6:100909000-100909400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:100909000-100909400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
37	chr6:100909000-100909600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:100909000-100909600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr6:100909000-100909600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:100909000-100909600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
41	chr6:100909000-100910200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:100909000-100910400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
43	chr6:100909200-100909400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
44	chr6:100909200-100909400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:100909200-100909400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:100909200-100909400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
47	chr6:100909200-100909400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:100909200-100909400	Bivalent Enhancer	Brain Germinal Matrix	brain
49	chr6:100909200-100909400	Bivalent Enhancer	Left Ventricle	heart
50	chr6:100909200-100909400	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion

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