Variant report

Variant	rs62140299
Chromosome Location	chr2:54763873-54763874
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54761550..54763887-chr2:54765151..54767469,2	K562	blood:
2	chr2:54763693..54765544-chr2:54775882..54778958,3	MCF-7	breast:
3	chr2:54759200..54761130-chr2:54762739..54764614,2	K562	blood:
4	chr2:54763015..54764801-chr2:54803765..54806395,2	K562	blood:
5	chr2:54760402..54763033-chr2:54763448..54765136,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11892709	1.00[ASN][1000 genomes]
rs17045859	1.00[ASN][1000 genomes]
rs17045866	1.00[ASN][1000 genomes]
rs187123	1.00[ASN][1000 genomes]
rs2666035	1.00[ASN][1000 genomes]
rs2931462	1.00[ASN][1000 genomes]
rs2941577	1.00[ASN][1000 genomes]
rs2941593	1.00[ASN][1000 genomes]
rs2941594	1.00[ASN][1000 genomes]
rs354212	1.00[ASN][1000 genomes]
rs354219	1.00[ASN][1000 genomes]
rs354221	1.00[ASN][1000 genomes]
rs354233	1.00[ASN][1000 genomes]
rs62140272	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140273	1.00[ASN][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	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv528848	chr2:54758305-54777576	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
2	chr2:54744000-54777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54744400-54769600	Weak transcription	Spleen	Spleen
4	chr2:54747200-54769800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54748400-54768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:54748400-54776800	Weak transcription	Pancreas	Pancrea
7	chr2:54750800-54769800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr2:54752000-54764600	Weak transcription	Gastric	stomach
9	chr2:54752200-54767600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:54752200-54777800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:54753800-54764800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr2:54753800-54768200	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:54754400-54767800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:54754800-54767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:54755000-54767600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:54756600-54764200	Weak transcription	Psoas Muscle	Psoas
17	chr2:54756800-54767600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:54757000-54767800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr2:54757000-54776800	Weak transcription	Brain Germinal Matrix	brain
20	chr2:54757400-54766200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:54757400-54771000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
23	chr2:54758600-54772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:54759600-54764000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:54760200-54768800	Genic enhancers	Left Ventricle	heart
26	chr2:54760400-54764000	Weak transcription	Ovary	ovary
27	chr2:54760400-54769600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:54760600-54765200	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:54760600-54766000	Weak transcription	Small Intestine	intestine
30	chr2:54760600-54767000	Weak transcription	NH-A	brain
31	chr2:54760800-54764000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:54760800-54767800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr2:54761000-54764800	Strong transcription	Fetal Stomach	stomach
34	chr2:54761000-54767000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:54761000-54769400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:54761200-54764000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:54761200-54768800	Strong transcription	HSMM	muscle
38	chr2:54761400-54766000	Weak transcription	Lung	lung
39	chr2:54761600-54764000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:54761600-54767200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:54761600-54773200	Weak transcription	Fetal Brain Male	brain
42	chr2:54761800-54766000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:54761800-54769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:54762000-54764600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:54762000-54766000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:54762000-54766800	Weak transcription	Right Ventricle	heart
47	chr2:54762000-54775400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:54762200-54764000	Weak transcription	Right Atrium	heart
49	chr2:54762200-54764400	Weak transcription	Fetal Lung	lung
50	chr2:54762200-54765800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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