Variant report

Variant	rs1356168
Chromosome Location	chr2:190018099-190018100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190012942..190018195-chr2:190085147..190088368,4	MCF-7	breast:
2	chr2:190011309..190014664-chr2:190015340..190018196,3	MCF-7	breast:
3	chr2:190010984..190012926-chr2:190016362..190018149,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1016622	0.83[YRI][hapmap]
rs10931400	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10931404	0.86[EUR][1000 genomes]
rs11681286	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11691604	0.83[CEU][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs12104769	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12105389	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12611950	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12615823	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12618438	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12621035	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12621806	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12621939	0.89[EUR][1000 genomes]
rs12991770	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12993719	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12995956	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999122	0.91[EUR][1000 genomes]
rs12999996	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13004722	0.82[EUR][1000 genomes]
rs13005652	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13005714	0.84[LWK][hapmap]
rs13005821	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13011374	0.84[EUR][1000 genomes]
rs13011485	0.82[EUR][1000 genomes]
rs13012327	0.86[EUR][1000 genomes]
rs13012649	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13015283	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs13016231	0.91[EUR][1000 genomes]
rs13017413	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13019076	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13021508	0.83[EUR][1000 genomes]
rs13022633	0.85[EUR][1000 genomes]
rs13028967	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13029705	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13030984	0.81[LWK][hapmap]
rs13031211	0.83[ASW][hapmap];1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13031549	0.92[CEU][hapmap];0.80[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13033421	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1356162	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1356163	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1356164	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1356165	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1356167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1399991	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1399992	0.86[EUR][1000 genomes]
rs1515874	0.86[EUR][1000 genomes]
rs1515876	0.86[EUR][1000 genomes]
rs1568334	0.82[EUR][1000 genomes]
rs1878085	0.92[EUR][1000 genomes]
rs1949327	0.81[LWK][hapmap]
rs1949484	0.91[EUR][1000 genomes]
rs1965422	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2138374	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222256	0.91[EUR][1000 genomes]
rs2351627	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2351636	0.82[EUR][1000 genomes]
rs35475196	0.86[EUR][1000 genomes]
rs3914778	0.91[EUR][1000 genomes]
rs4233801	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4417749	0.81[LWK][hapmap]
rs4428040	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4667266	0.83[YRI][hapmap]
rs4667272	0.91[EUR][1000 genomes]
rs4667274	0.86[EUR][1000 genomes]
rs4667276	0.82[EUR][1000 genomes]
rs4667277	0.82[EUR][1000 genomes]
rs4998559	1.00[CEU][hapmap];0.80[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60124911	0.92[EUR][1000 genomes]
rs62182416	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434339	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6708419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6714088	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6719104	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6737071	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752781	0.80[JPT][hapmap]
rs7419888	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7561002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7564611	0.85[EUR][1000 genomes]
rs7576165	0.92[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs7587147	0.91[EUR][1000 genomes]
rs7587956	0.91[EUR][1000 genomes]
rs7607133	0.86[EUR][1000 genomes]
rs7609495	0.86[EUR][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
rs1356168	COL5A2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190011200-190020800	Enhancers	NHDF-Ad	bronchial
2	chr2:190014600-190019200	Enhancers	NHLF	lung
3	chr2:190015200-190026600	Weak transcription	Liver	Liver
4	chr2:190016000-190028200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:190016200-190018600	Enhancers	Adipose Nuclei	Adipose
6	chr2:190016200-190019200	Enhancers	Fetal Lung	lung
7	chr2:190016200-190027000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:190016800-190018400	Enhancers	Stomach Smooth Muscle	stomach
9	chr2:190016800-190018800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:190016800-190018800	Enhancers	Colon Smooth Muscle	Colon
11	chr2:190016800-190018800	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr2:190017000-190018200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:190017000-190018400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:190017000-190018800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:190017000-190018800	Enhancers	Ovary	ovary
16	chr2:190017000-190019400	Enhancers	Fetal Stomach	stomach
17	chr2:190017200-190018600	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:190017200-190018800	Enhancers	Aorta	Aorta
19	chr2:190017400-190018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:190017400-190018600	Weak transcription	Fetal Heart	heart
21	chr2:190017400-190018600	Enhancers	Fetal Kidney	kidney
22	chr2:190017400-190019000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:190017400-190023200	Weak transcription	HSMMtube	muscle
24	chr2:190017600-190018800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:190017600-190019200	Enhancers	Osteobl	bone
26	chr2:190017600-190020800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:190017600-190028800	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:190017800-190018200	Flanking Active TSS	A549	lung
29	chr2:190017800-190019000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:190017800-190019000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:190017800-190020000	Weak transcription	HSMM	muscle
32	chr2:190018000-190018400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:190018000-190018400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:190018000-190018600	Genic enhancers	NH-A	brain
35	chr2:190018000-190018800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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