Variant report

Variant	rs1878085
Chromosome Location	chr2:190073366-190073367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190071758..190073666-chr2:190084082..190085954,2	K562	blood:
2	chr2:190070733..190073689-chr2:190074738..190076938,2	MCF-7	breast:
3	chr2:190064765..190067723-chr2:190072988..190074631,2	K562	blood:
4	chr2:190069482..190073456-chr2:190088390..190091249,3	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10181597	0.84[CHD][hapmap]
rs10194682	0.87[CHD][hapmap]
rs10931400	0.91[EUR][1000 genomes]
rs10931404	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11681286	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691604	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12104769	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12105389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12611950	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12615823	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618438	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621035	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621806	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621939	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12991770	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12993719	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12995956	0.91[EUR][1000 genomes]
rs12999122	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12999996	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13004187	0.82[EUR][1000 genomes]
rs13004722	0.90[EUR][1000 genomes]
rs13005652	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13005821	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13011374	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13011485	0.90[EUR][1000 genomes]
rs13012327	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13012649	0.90[EUR][1000 genomes]
rs13015283	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13016231	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017413	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13019076	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13021508	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13022633	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13028967	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13029705	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13031211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031549	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13033421	0.91[EUR][1000 genomes]
rs1356162	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356163	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1356164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1356165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1356167	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1356168	1.00[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs1399991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1399992	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1515874	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1515876	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520859	0.83[EUR][1000 genomes]
rs1568334	0.90[EUR][1000 genomes]
rs1949484	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1965422	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138374	0.92[CEU][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2222256	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2351627	0.91[EUR][1000 genomes]
rs2351636	0.90[EUR][1000 genomes]
rs35475196	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35772309	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3914778	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233801	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4428040	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4666774	0.81[EUR][1000 genomes]
rs4667264	1.00[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4667265	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4667272	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4667274	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667276	0.90[EUR][1000 genomes]
rs4667277	0.90[EUR][1000 genomes]
rs4998559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60124911	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62182416	0.86[EUR][1000 genomes]
rs6434317	0.84[CHD][hapmap]
rs6434318	0.84[CHD][hapmap]
rs6434339	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs6708419	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6714088	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6719104	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6737071	0.92[EUR][1000 genomes]
rs6738371	0.87[CHD][hapmap]
rs7419888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7561002	1.00[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7564611	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7576165	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7587147	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7587956	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7607133	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7609495	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1878085	COL5A2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190069800-190073600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:190069800-190074400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:190070000-190074600	Weak transcription	HMEC	breast
4	chr2:190070200-190074000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:190070200-190074200	Weak transcription	NHEK	skin
6	chr2:190070400-190074400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:190071200-190075000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:190072200-190074800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:190072600-190074800	Enhancers	Adipose Nuclei	Adipose
10	chr2:190072600-190076000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:190072800-190073800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:190072800-190074600	Enhancers	NHDF-Ad	bronchial
13	chr2:190072800-190074600	Enhancers	Osteobl	bone
14	chr2:190072800-190074800	Enhancers	HUVEC	blood vessel
15	chr2:190072800-190074800	Enhancers	NHLF	lung
16	chr2:190072800-190075000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:190072800-190075800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:190073000-190073400	Transcr. at gene 5' and 3'	A549	lung
19	chr2:190073000-190073800	Enhancers	K562	blood
20	chr2:190073000-190074400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:190073000-190074600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:190073000-190075400	Enhancers	Hela-S3	cervix
23	chr2:190073000-190077000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:190073000-190077000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:190073200-190073400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:190073200-190073400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:190073200-190073400	Enhancers	Fetal Lung	lung
28	chr2:190073200-190073600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr2:190073200-190073600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:190073200-190073600	Weak transcription	Aorta	Aorta
31	chr2:190073200-190073800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr2:190073200-190073800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:190073200-190073800	Enhancers	Ovary	ovary
34	chr2:190073200-190074600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:190073200-190074800	Enhancers	NH-A	brain
36	chr2:190073200-190075400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:190073200-190075400	Enhancers	Fetal Stomach	stomach
38	chr2:190073200-190075400	Enhancers	HSMM	muscle
39	chr2:190073200-190075800	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr2:190073200-190077000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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