Variant report

Variant	rs6739988
Chromosome Location	chr2:11518500-11518501
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11518112..11520070-chr2:11527868..11530807,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231403	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10803734	1.00[EUR][1000 genomes]
rs13410951	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs16857295	1.00[CEU][hapmap]
rs16857649	1.00[CEU][hapmap]
rs4668728	1.00[EUR][1000 genomes]
rs4669732	1.00[EUR][1000 genomes]
rs4669734	1.00[EUR][1000 genomes]
rs56239196	1.00[EUR][1000 genomes]
rs56252168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56273175	1.00[EUR][1000 genomes]
rs57251854	1.00[EUR][1000 genomes]
rs58477298	1.00[EUR][1000 genomes]
rs58819315	1.00[EUR][1000 genomes]
rs59554925	1.00[EUR][1000 genomes]
rs60798771	1.00[EUR][1000 genomes]
rs61091666	1.00[EUR][1000 genomes]
rs61358269	1.00[EUR][1000 genomes]
rs6432204	1.00[EUR][1000 genomes]
rs6432205	1.00[EUR][1000 genomes]
rs6432206	1.00[EUR][1000 genomes]
rs6432217	1.00[CEU][hapmap]
rs6432218	1.00[CEU][hapmap]
rs6710070	1.00[EUR][1000 genomes]
rs6712902	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6740248	1.00[CEU][hapmap]
rs73180141	1.00[EUR][1000 genomes]
rs73915200	1.00[EUR][1000 genomes]
rs73915202	1.00[EUR][1000 genomes]
rs73917203	1.00[EUR][1000 genomes]
rs73917206	1.00[EUR][1000 genomes]
rs73917207	1.00[EUR][1000 genomes]
rs7559230	1.00[EUR][1000 genomes]
rs7565382	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7598673	1.00[EUR][1000 genomes]
rs7608777	1.00[CEU][hapmap];1.00[EUR][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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11514800-11519200	Enhancers	Fetal Intestine Large	intestine
2	chr2:11515200-11519000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:11515400-11518600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:11515400-11520000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:11515400-11526000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:11515600-11519200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:11515600-11519400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:11515600-11520000	Weak transcription	Liver	Liver
9	chr2:11515800-11519200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:11515800-11519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:11515800-11519400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:11515800-11519600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:11515800-11519600	Weak transcription	NHEK	skin
14	chr2:11515800-11520000	Weak transcription	Fetal Heart	heart
15	chr2:11516000-11518600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:11516000-11526000	Weak transcription	Aorta	Aorta
17	chr2:11516200-11518600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:11516200-11518600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:11516200-11518600	Weak transcription	Small Intestine	intestine
20	chr2:11516200-11519000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:11516200-11519400	Weak transcription	HMEC	breast
22	chr2:11516200-11522400	Weak transcription	Hela-S3	cervix
23	chr2:11516200-11528400	Weak transcription	Pancreas	Pancrea
24	chr2:11516800-11518600	Weak transcription	Fetal Thymus	thymus
25	chr2:11516800-11519400	Enhancers	HepG2	liver
26	chr2:11517200-11518800	Weak transcription	Spleen	Spleen
27	chr2:11517200-11519000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:11517200-11519400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:11517200-11519400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:11517200-11519800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:11517600-11519200	Enhancers	Psoas Muscle	Psoas
32	chr2:11517600-11519800	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:11517600-11520000	Enhancers	Fetal Stomach	stomach
34	chr2:11517600-11520000	Enhancers	Lung	lung
35	chr2:11517600-11536400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:11517800-11520200	Enhancers	Fetal Muscle Leg	muscle
37	chr2:11518000-11518800	Flanking Active TSS	NHLF	lung
38	chr2:11518000-11519000	Enhancers	Primary B cells from cord blood	blood
39	chr2:11518000-11520200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:11518000-11520200	Enhancers	Placenta	Placenta
41	chr2:11518200-11518600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:11518200-11518600	Active TSS	Colonic Mucosa	Colon
43	chr2:11518200-11518600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr2:11518200-11518600	Flanking Active TSS	Fetal Lung	lung
45	chr2:11518200-11518600	Enhancers	HSMM	muscle
46	chr2:11518200-11518800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:11518200-11518800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:11518200-11518800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr2:11518200-11518800	Active TSS	Adipose Nuclei	Adipose
50	chr2:11518200-11518800	Enhancers	Brain Angular Gyrus	brain

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