Variant report

Variant	rs3890574
Chromosome Location	chr2:189298316-189298317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10167709	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10170220	0.94[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10174928	0.81[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10179504	0.82[EUR][1000 genomes]
rs10180687	0.88[EUR][1000 genomes]
rs10180956	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10182377	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10185828	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10192374	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198025	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10199264	0.84[EUR][1000 genomes]
rs10204674	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10206167	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10209733	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10210696	0.82[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10211189	0.81[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931355	0.81[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10931358	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10931359	0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1125099	0.94[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11682085	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12151691	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12329399	0.81[CEU][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12465164	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12465625	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs12473653	0.83[ASN][1000 genomes]
rs12474692	0.80[CHB][hapmap]
rs12624002	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12693498	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12987194	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs12990374	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13384413	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13387350	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13388723	0.84[EUR][1000 genomes]
rs13388746	0.81[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13389155	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13389879	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13394421	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13412312	0.84[EUR][1000 genomes]
rs13415123	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13420369	0.93[CEU][hapmap];0.91[JPT][hapmap]
rs13422246	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13422836	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13423891	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13424536	0.93[JPT][hapmap]
rs13426709	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13427070	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28542209	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28564315	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4261684	0.89[EUR][1000 genomes]
rs4274570	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4340469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4349309	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4361092	1.00[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs4381754	0.81[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4398237	0.93[JPT][hapmap]
rs4430902	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs4433962	0.81[CEU][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4458180	1.00[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4476318	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4513258	0.93[JPT][hapmap]
rs4522565	0.81[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4640356	1.00[CEU][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs4666758	0.81[CHD][hapmap];0.93[JPT][hapmap]
rs4667225	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667226	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4992744	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs55693630	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56072532	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58966470	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58978246	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59206116	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60796263	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62183212	0.80[ASN][1000 genomes]
rs6434280	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66732509	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs66923332	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704814	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67086516	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67092191	0.84[EUR][1000 genomes]
rs67240894	0.89[EUR][1000 genomes]
rs6725860	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6727850	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6729182	0.93[JPT][hapmap]
rs6732963	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6737728	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6739162	0.81[CEU][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6743120	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743636	0.94[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6756220	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6761769	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761785	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67750782	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67798410	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67919447	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72907672	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73040452	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7420700	0.81[CEU][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7561448	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7566619	0.81[CHD][hapmap]
rs7574262	0.81[CHD][hapmap]
rs7579610	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7593215	0.81[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7595327	0.87[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595377	0.94[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7606178	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7607063	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9288157	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9808557	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv533786	chr2:189248503-189354495	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3890574	COL3A1	cis	parietal	SCAN
rs3890574	MYO1B	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189285600-189318800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:189285800-189318200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:189292400-189306200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:189293600-189308800	Weak transcription	HUVEC	blood vessel
5	chr2:189294200-189308000	Weak transcription	Ovary	ovary
6	chr2:189295200-189298800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr2:189295600-189304200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:189297200-189299200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:189297400-189299200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr2:189297600-189298600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:189297600-189298800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:189297600-189299000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr2:189297800-189299200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:189297800-189303800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:189298000-189298800	Enhancers	H1 Cell Line	embryonic stem cell

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