Variant report

Variant	rs62182454
Chromosome Location	chr2:190039575-190039576
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190039205..190041419-chr2:190045253..190047798,2	MCF-7	breast:
2	chr2:190036925..190039844-chr2:190040601..190043479,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10497699	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10931402	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931406	0.89[ASN][1000 genomes]
rs10931410	0.89[ASN][1000 genomes]
rs11675295	0.89[ASN][1000 genomes]
rs11676812	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11678388	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11684869	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12472232	0.83[ASN][1000 genomes]
rs1515873	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1515875	0.80[ASN][1000 genomes]
rs17198773	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17198780	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17198787	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17198829	0.89[ASN][1000 genomes]
rs17270952	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17270966	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17270973	0.86[ASN][1000 genomes]
rs17270987	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17271008	0.83[ASN][1000 genomes]
rs35598715	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55726777	0.89[ASN][1000 genomes]
rs55851872	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56252219	0.83[ASN][1000 genomes]
rs59031473	0.89[ASN][1000 genomes]
rs61130121	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62182415	0.89[ASN][1000 genomes]
rs62182420	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62182421	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62182457	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182458	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62182459	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62183794	0.89[ASN][1000 genomes]
rs62183841	0.89[ASN][1000 genomes]
rs62183844	0.89[ASN][1000 genomes]
rs62183845	0.89[ASN][1000 genomes]
rs72908368	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72908382	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72910347	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72910360	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7586853	0.83[ASN][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:190029400-190040800	Weak transcription	Fetal Kidney	kidney
3	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
6	chr2:190030000-190041200	Weak transcription	HUVEC	blood vessel
7	chr2:190030200-190041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:190034000-190040800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:190034000-190043400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:190034200-190041400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:190034800-190040400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:190036200-190040600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:190037000-190040400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:190037000-190040400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:190037000-190040800	Weak transcription	Right Atrium	heart
17	chr2:190037000-190041000	Weak transcription	Ovary	ovary
18	chr2:190037200-190039800	Weak transcription	Adipose Nuclei	Adipose
19	chr2:190037200-190040600	Weak transcription	Fetal Lung	lung
20	chr2:190037400-190039600	Weak transcription	HSMMtube	muscle
21	chr2:190037400-190039800	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:190037400-190040400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:190037400-190040800	Weak transcription	Fetal Heart	heart
24	chr2:190037400-190040800	Weak transcription	Fetal Stomach	stomach
25	chr2:190037400-190041200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:190037400-190041400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:190037400-190042600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:190037400-190042600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:190038200-190039800	Strong transcription	NH-A	brain
30	chr2:190038600-190039600	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr2:190038600-190040000	Strong transcription	HSMM	muscle
32	chr2:190038600-190040000	Genic enhancers	NHDF-Ad	bronchial
33	chr2:190038600-190040600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:190038800-190039800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:190038800-190040200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:190038800-190040200	Genic enhancers	Osteobl	bone
37	chr2:190038800-190040600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:190038800-190040600	Genic enhancers	A549	lung
39	chr2:190038800-190040800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:190039000-190039800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:190039200-190039600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:190039200-190040400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:190039200-190040800	Weak transcription	Aorta	Aorta
44	chr2:190039200-190040800	Weak transcription	NHLF	lung
45	chr2:190039400-190039600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:190039400-190039800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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