Variant report

Variant	rs1520856
Chromosome Location	chr2:190276973-190276974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:189979724..189980417-chr2:190276740..190277610,3	MCF-7	breast:
2	chr2:189958956..189959638-chr2:190276828..190277345,2	MCF-7	breast:
3	chr2:190007607..190008525-chr2:190276403..190277763,5	MCF-7	breast:
4	chr2:189959134..189959659-chr2:190276784..190277316,2	K562	blood:
5	chr2:189389248..189389928-chr2:190276695..190277389,2	K562	blood:
6	chr2:189848219..189848800-chr2:190276497..190277312,2	MCF-7	breast:
7	chr2:189378325..189379323-chr2:190276804..190277370,2	K562	blood:
8	chr2:190007614..190008526-chr2:190276902..190277807,3	K562	blood:

No data

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10166420	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10188246	0.84[ASN][1000 genomes]
rs10198663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10210634	0.98[ASN][1000 genomes]
rs10804029	0.90[ASN][1000 genomes]
rs10931411	0.84[EUR][1000 genomes]
rs10931417	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11676905	0.84[ASN][1000 genomes]
rs11677167	0.98[ASN][1000 genomes]
rs11678414	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613903	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12622720	0.83[ASN][1000 genomes]
rs12623394	0.80[ASN][1000 genomes]
rs12693539	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693540	0.83[ASN][1000 genomes]
rs12994482	0.84[ASN][1000 genomes]
rs13009912	0.87[ASN][1000 genomes]
rs13015207	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13018252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13035381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356976	1.00[ASN][1000 genomes]
rs1520854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520858	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1520866	0.85[ASN][1000 genomes]
rs1595749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16831454	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1851104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1866605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1898971	0.83[ASN][1000 genomes]
rs1992295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304702	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2351932	0.86[ASN][1000 genomes]
rs2351934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2683012	0.86[ASN][1000 genomes]
rs2882805	0.92[ASN][1000 genomes]
rs4309611	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4580411	0.95[ASN][1000 genomes]
rs4666775	0.89[ASN][1000 genomes]
rs4667275	0.84[EUR][1000 genomes]
rs4667280	0.96[ASN][1000 genomes]
rs4667284	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6434340	0.95[ASN][1000 genomes]
rs6434342	0.93[ASN][1000 genomes]
rs6434343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738193	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6747222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6752545	0.98[ASN][1000 genomes]
rs734859	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7420765	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7422875	0.84[ASN][1000 genomes]
rs7425383	0.84[ASN][1000 genomes]
rs744556	0.80[ASN][1000 genomes]
rs745742	0.83[ASN][1000 genomes]
rs7556928	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7566093	0.98[ASN][1000 genomes]
rs7574403	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7590098	0.85[AMR][1000 genomes]
rs8179541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs893407	0.83[ASN][1000 genomes]
rs893408	0.80[ASN][1000 genomes]
rs9677436	0.93[AFR][1000 genomes];0.98[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	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
3	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1520856	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190273000-190277600	Enhancers	NH-A	brain
2	chr2:190273000-190277800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:190273000-190286200	Weak transcription	Aorta	Aorta
4	chr2:190273200-190277600	Enhancers	NHDF-Ad	bronchial
5	chr2:190273200-190277800	Enhancers	Colon Smooth Muscle	Colon
6	chr2:190273200-190278400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:190273400-190277800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:190274200-190277600	Weak transcription	Fetal Stomach	stomach
9	chr2:190275400-190278200	Enhancers	NHLF	lung
10	chr2:190275800-190277800	Enhancers	Rectal Smooth Muscle	rectum
11	chr2:190276000-190277200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:190276000-190277200	Enhancers	Adipose Nuclei	Adipose
13	chr2:190276000-190277200	Enhancers	HUVEC	blood vessel
14	chr2:190276000-190277600	Enhancers	A549	lung
15	chr2:190276000-190277800	Enhancers	Fetal Lung	lung
16	chr2:190276000-190277800	Enhancers	Osteobl	bone
17	chr2:190276200-190277000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:190276200-190277000	Enhancers	HMEC	breast
19	chr2:190276200-190277200	Enhancers	Primary T cells from cord blood	blood
20	chr2:190276400-190277000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:190276400-190277000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr2:190276400-190277000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:190276400-190277400	Weak transcription	HSMM	muscle
24	chr2:190276400-190277600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr2:190276600-190277000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr2:190276600-190277000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:190276600-190277000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:190276600-190277000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr2:190276600-190277000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:190276600-190277000	Active TSS	Ovary	ovary
31	chr2:190276600-190277000	Enhancers	Psoas Muscle	Psoas
32	chr2:190276600-190277000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:190276600-190277000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:190276600-190277000	Enhancers	HSMMtube	muscle
35	chr2:190276600-190277000	Enhancers	NHEK	skin
36	chr2:190276800-190277000	Enhancers	Fetal Muscle Leg	muscle
37	chr2:190276800-190277200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:190276800-190277200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:190276800-190277200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:190276800-190277600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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