Variant report

Variant	rs1949604
Chromosome Location	chr2:190215928-190215929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10187060	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs10497700	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10497703	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs10755004	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10931414	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931415	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931416	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10931418	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10931419	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1112578	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1157910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11677066	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11688021	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11691604	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11691691	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11695159	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12105389	0.92[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs12612412	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12613876	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs12616234	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12623723	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12987962	0.81[EUR][1000 genomes]
rs12988143	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs12990035	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12990235	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12997620	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13004187	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13004722	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13010531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13011374	0.86[EUR][1000 genomes]
rs13011485	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015203	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13015283	0.87[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13021508	0.83[EUR][1000 genomes]
rs13022633	0.85[EUR][1000 genomes]
rs13031211	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap]
rs13031549	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs13032853	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13033841	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1356164	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1356165	0.92[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap]
rs1356167	0.92[CEU][hapmap]
rs1356168	0.92[CEU][hapmap];0.89[TSI][hapmap]
rs1356977	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1399991	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1402368	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1520855	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1520857	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1520859	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1520863	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1520864	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1568334	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1581351	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1851105	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1949605	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965422	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs2304703	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2351636	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4287797	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4353589	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666774	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667274	0.83[EUR][1000 genomes]
rs4667276	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667277	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667281	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4667284	0.81[JPT][hapmap]
rs4998559	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs6434339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6708419	0.92[CEU][hapmap]
rs6728055	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6745108	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7419276	0.84[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7419888	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7564611	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7576165	0.80[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.86[EUR][1000 genomes]
rs7588453	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7593821	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7596592	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7607133	0.83[EUR][1000 genomes]
rs963738	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9679659	0.90[AMR][1000 genomes];0.94[EUR][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	nsv875614	chr2:190110841-190254758	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1949604	COL5A2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190214600-190216000	Enhancers	Rectal Smooth Muscle	rectum
2	chr2:190214600-190216200	Enhancers	NHDF-Ad	bronchial
3	chr2:190214600-190216400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr2:190214800-190216400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:190215000-190216000	Enhancers	NH-A	brain
6	chr2:190215000-190216200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:190215000-190216200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:190215200-190216000	Enhancers	Colon Smooth Muscle	Colon
9	chr2:190215200-190216000	Enhancers	Ovary	ovary
10	chr2:190215200-190216000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:190215200-190216000	Enhancers	HUVEC	blood vessel
12	chr2:190215200-190216200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:190215200-190216200	Enhancers	HSMM	muscle
14	chr2:190215200-190216200	Enhancers	NHLF	lung
15	chr2:190215200-190216200	Enhancers	Osteobl	bone
16	chr2:190215400-190216000	Enhancers	Stomach Mucosa	stomach
17	chr2:190215600-190216000	Enhancers	HSMMtube	muscle
18	chr2:190215800-190228400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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