Variant report

Variant	rs6709123
Chromosome Location	chr2:63962974-63962975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:63816189..63818195-chr2:63961769..63963373,2	MCF-7	breast:
2	chr2:63960179..63963716-chr2:63967320..63970574,3	MCF-7	breast:
3	chr2:63960746..63963454-chr2:64068173..64070069,3	MCF-7	breast:
4	chr2:63961867..63963389-chr2:63963421..63965868,2	MCF-7	breast:
5	chr2:63955758..63957813-chr2:63962265..63964791,2	MCF-7	breast:
6	chr2:63960550..63964590-chr2:64064036..64069240,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000014641	Chromatin interaction
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs60746057	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704778	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6732191	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7585588	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6709123	BCL11A	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63955600-63963600	Weak transcription	Aorta	Aorta
2	chr2:63955600-63964200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:63957400-63968200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:63957400-63971200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:63961200-63966200	Enhancers	Liver	Liver
6	chr2:63961600-63966000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:63961800-63965800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:63962000-63965800	Enhancers	Osteobl	bone
9	chr2:63962200-63965400	Enhancers	Adipose Nuclei	Adipose
10	chr2:63962200-63966000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:63962400-63963000	Flanking Active TSS	HUVEC	blood vessel
12	chr2:63962400-63963400	Enhancers	A549	lung
13	chr2:63962400-63963400	Enhancers	NHLF	lung
14	chr2:63962400-63964200	Enhancers	NHEK	skin
15	chr2:63962400-63964400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:63962400-63964800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:63962400-63964800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:63962400-63964800	Enhancers	NH-A	brain
19	chr2:63962400-63965000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:63962400-63965000	Enhancers	Fetal Lung	lung
21	chr2:63962400-63965400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr2:63962400-63965400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:63962400-63965400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr2:63962400-63965400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:63962400-63965600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:63962400-63965800	Enhancers	NHDF-Ad	bronchial
27	chr2:63962400-63966000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:63962400-63966000	Enhancers	HMEC	breast
29	chr2:63962600-63964000	Enhancers	HepG2	liver
30	chr2:63962600-63964200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:63962600-63964200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:63962600-63964400	Enhancers	Hela-S3	cervix
33	chr2:63962800-63963000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:63962800-63963200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:63962800-63964000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:63962800-63964000	Weak transcription	Ovary	ovary
37	chr2:63962800-63964200	Weak transcription	Pancreas	Pancrea
38	chr2:63962800-63964200	Weak transcription	Psoas Muscle	Psoas

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