Variant report

Variant	rs1990609
Chromosome Location	chr2:40667007-40667008
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	chr2:40662045..40663958-chr2:40665740..40668580,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11901878	0.84[CEU][hapmap]
rs13031545	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs13031785	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs13031843	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs13031849	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs13035085	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs17025999	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs17026001	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs17026005	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs17026009	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs17026011	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs17026012	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs17026014	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs17026018	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1990610	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2888678	0.81[CEU][hapmap]
rs4366950	0.84[CEU][hapmap]
rs4993292	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];0.95[YRI][hapmap]
rs6737745	0.82[CEU][hapmap]
rs6749800	0.82[EUR][1000 genomes]
rs7598773	0.84[CEU][hapmap]
rs7603114	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40646600-40670800	Weak transcription	Fetal Brain Female	brain
2	chr2:40648000-40667200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:40648200-40676400	Weak transcription	Fetal Kidney	kidney
4	chr2:40653000-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:40657000-40671200	Weak transcription	Fetal Stomach	stomach
6	chr2:40662600-40667800	Weak transcription	Primary B cells from cord blood	blood
7	chr2:40662600-40677200	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:40663400-40672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:40663600-40677000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:40663600-40677000	Weak transcription	Aorta	Aorta
11	chr2:40663800-40667800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:40663800-40677600	Weak transcription	HSMMtube	muscle
13	chr2:40664200-40667400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:40664200-40667800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:40664400-40667200	Enhancers	NHDF-Ad	bronchial
16	chr2:40664600-40667600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr2:40664600-40673000	Weak transcription	Left Ventricle	heart
18	chr2:40665000-40668200	Enhancers	Osteobl	bone
19	chr2:40665200-40667800	Enhancers	HSMM	muscle
20	chr2:40665200-40668400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:40665200-40668600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:40665200-40675200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:40665400-40674800	Weak transcription	NHLF	lung
24	chr2:40665800-40668000	Weak transcription	Dnd41	blood
25	chr2:40666600-40673400	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:40666600-40676400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:40666600-40676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:40666600-40677200	Weak transcription	Right Ventricle	heart
29	chr2:40666800-40671200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:40666800-40675400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:40667000-40667200	Enhancers	Fetal Heart	heart
32	chr2:40667000-40670000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:40667000-40672400	Weak transcription	Brain Anterior Caudate	brain
34	chr2:40667000-40676200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:40667000-40676400	Weak transcription	HMEC	breast

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