Variant report

Variant	rs1520857
Chromosome Location	chr2:190273464-190273465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190271223..190274558-chr2:190305848..190310327,4	K562	blood:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10187060	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs10497700	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497703	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs10755004	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10931414	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10931415	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10931416	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10931418	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931419	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112578	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1157910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11677066	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691691	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11695159	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12612412	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12613876	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12616234	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12623723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12987962	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12988143	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs12990035	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12990235	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997620	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004187	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13004722	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13010531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13011374	0.80[EUR][1000 genomes]
rs13011485	0.82[EUR][1000 genomes]
rs13015203	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13015283	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs13032853	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13033841	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1356977	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1402368	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1520855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1520859	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1520863	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1520864	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1568334	0.82[EUR][1000 genomes]
rs1581351	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1851105	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1949604	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1949605	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2119069	0.86[ASN][1000 genomes]
rs2304703	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2351636	0.81[EUR][1000 genomes]
rs35997606	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4287797	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353589	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4666774	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4667276	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4667277	0.82[EUR][1000 genomes]
rs4667281	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667284	0.86[LWK][hapmap]
rs6434339	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs6728055	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745108	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419276	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7576165	0.80[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.80[EUR][1000 genomes]
rs7588453	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7593821	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7596592	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963738	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9679659	0.97[AMR][1000 genomes];0.99[EUR][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
rs1520857	COL5A2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190268200-190276800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:190269200-190275000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:190270400-190274400	Enhancers	Rectal Smooth Muscle	rectum
4	chr2:190271400-190274200	Enhancers	Fetal Stomach	stomach
5	chr2:190272200-190273600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:190272600-190273600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:190272600-190276400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:190272600-190276600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:190272600-190276600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:190272800-190273800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:190272800-190274800	Enhancers	HSMM	muscle
12	chr2:190272800-190276600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:190273000-190273600	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr2:190273000-190275000	Enhancers	A549	lung
15	chr2:190273000-190275600	Enhancers	Osteobl	bone
16	chr2:190273000-190276000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:190273000-190276400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:190273000-190277600	Enhancers	NH-A	brain
19	chr2:190273000-190277800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:190273000-190286200	Weak transcription	Aorta	Aorta
21	chr2:190273200-190274000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:190273200-190274000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:190273200-190274000	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:190273200-190274200	Enhancers	NHLF	lung
25	chr2:190273200-190274600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:190273200-190275200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:190273200-190275600	Enhancers	HUVEC	blood vessel
28	chr2:190273200-190276000	Weak transcription	Adipose Nuclei	Adipose
29	chr2:190273200-190276000	Weak transcription	Fetal Lung	lung
30	chr2:190273200-190276200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:190273200-190276200	Weak transcription	Primary T cells from cord blood	blood
32	chr2:190273200-190276200	Weak transcription	HMEC	breast
33	chr2:190273200-190276600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:190273200-190276600	Weak transcription	Ovary	ovary
35	chr2:190273200-190276600	Weak transcription	HSMMtube	muscle
36	chr2:190273200-190276600	Weak transcription	NHEK	skin
37	chr2:190273200-190276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:190273200-190277600	Enhancers	NHDF-Ad	bronchial
39	chr2:190273200-190277800	Enhancers	Colon Smooth Muscle	Colon
40	chr2:190273200-190278400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:190273400-190276000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:190273400-190276600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:190273400-190277800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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