Variant report

Variant	rs10497699
Chromosome Location	chr2:190032578-190032579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10931402	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931406	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931410	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11675295	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11676812	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11677073	0.90[ASN][1000 genomes]
rs11678388	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11681937	0.90[ASN][1000 genomes]
rs11684417	0.90[ASN][1000 genomes]
rs11684869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11687908	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11690774	0.95[EUR][1000 genomes]
rs11693810	0.90[ASN][1000 genomes]
rs11695837	0.88[EUR][1000 genomes]
rs12472232	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1515873	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1515875	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1519185	0.90[ASN][1000 genomes]
rs1520862	0.90[ASN][1000 genomes]
rs17198773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17198780	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17198787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17198815	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17198829	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17270952	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17270966	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17270973	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17270987	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17271008	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17271015	0.90[ASN][1000 genomes]
rs1996576	0.90[ASN][1000 genomes]
rs2683013	0.90[ASN][1000 genomes]
rs2683014	0.90[ASN][1000 genomes]
rs28413975	0.84[ASN][1000 genomes]
rs35598715	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55851872	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56252219	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56381644	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59031473	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61130121	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61528955	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182060	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182061	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182066	0.90[ASN][1000 genomes]
rs62182068	0.90[ASN][1000 genomes]
rs62182069	0.90[ASN][1000 genomes]
rs62182415	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182420	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62182421	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62182454	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62182457	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62182458	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182459	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62183794	0.90[ASN][1000 genomes]
rs62183841	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62183844	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62183845	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62183846	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62183847	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62183848	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72908368	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72908382	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72910347	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72910360	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72912280	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72912286	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72914135	0.84[ASN][1000 genomes]
rs72914141	0.90[ASN][1000 genomes]
rs7419543	1.00[CHD][hapmap]
rs7564429	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7586853	0.90[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10497699	COL5A2	cis	cerebellum	SCAN
rs10497699	COL5A2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:190028000-190032800	Enhancers	NHLF	lung
3	chr2:190028400-190033800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:190028800-190034200	Enhancers	Liver	Liver
5	chr2:190029000-190033600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:190029000-190037200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:190029200-190033600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:190029400-190040800	Weak transcription	Fetal Kidney	kidney
9	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:190029600-190032600	Enhancers	Fetal Muscle Leg	muscle
11	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:190029800-190033600	Enhancers	A549	lung
13	chr2:190029800-190036800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
15	chr2:190030000-190036600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:190030000-190041200	Weak transcription	HUVEC	blood vessel
17	chr2:190030200-190034400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:190030200-190041200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:190030400-190036600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:190030400-190043400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:190030600-190033600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:190030600-190033600	Weak transcription	Fetal Stomach	stomach
23	chr2:190030600-190033800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:190030600-190033800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:190031400-190032600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:190031600-190033800	Weak transcription	Right Atrium	heart
27	chr2:190031600-190038800	Weak transcription	Aorta	Aorta
28	chr2:190031800-190032600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr2:190031800-190033000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:190031800-190035200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:190032000-190033000	Weak transcription	HSMM	muscle
32	chr2:190032000-190033600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:190032000-190033600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:190032000-190033600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:190032000-190033600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:190032000-190033600	Weak transcription	Ovary	ovary
37	chr2:190032000-190033600	Enhancers	NHDF-Ad	bronchial
38	chr2:190032000-190035000	Weak transcription	NH-A	brain
39	chr2:190032000-190036000	Weak transcription	Fetal Lung	lung
40	chr2:190032000-190036600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:190032000-190036600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:190032200-190033600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:190032200-190033600	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:190032200-190033600	Weak transcription	HSMMtube	muscle
45	chr2:190032200-190034600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr2:190032400-190032800	Weak transcription	Adipose Nuclei	Adipose
47	chr2:190032400-190033600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:190032400-190033600	Weak transcription	Osteobl	bone

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