Variant report

Variant	rs9287990
Chromosome Location	chr2:152516831-152516832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152511087..152513556-chr2:152516616..152519080,2	K562	blood:
2	chr2:152511087..152512824-chr2:152516616..152519176,2	K562	blood:
3	chr2:152514466..152519197-chr2:152519383..152523165,5	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10167462	0.94[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs10170273	1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10178880	1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs10193188	0.94[CEU][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs1054883	0.87[CEU][hapmap];0.81[GIH][hapmap]
rs10930723	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10930740	0.83[EUR][1000 genomes]
rs11695661	0.94[CEU][hapmap];0.86[GIH][hapmap]
rs11904536	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12052828	0.93[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs12328501	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12464543	0.94[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs12472627	0.85[GIH][hapmap]
rs12616767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618063	0.87[GIH][hapmap]
rs12620077	1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12693090	0.83[EUR][1000 genomes]
rs13032138	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13404704	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13428975	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1357468	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs1799	0.87[CEU][hapmap];0.81[GIH][hapmap]
rs2344733	0.87[CEU][hapmap];0.95[JPT][hapmap]
rs4077121	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4077122	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4273217	0.93[CEU][hapmap]
rs4289189	0.83[EUR][1000 genomes]
rs4300824	0.90[GIH][hapmap]
rs4374369	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs4375863	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4381781	0.94[CEU][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs4413159	0.94[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4414677	0.85[GIH][hapmap]
rs4425075	0.94[CEU][hapmap];0.80[JPT][hapmap]
rs4453694	0.82[GIH][hapmap]
rs4465763	0.93[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs4536649	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4564765	0.95[EUR][1000 genomes]
rs4564766	0.94[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs4611637	0.94[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4614931	0.94[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap]
rs4625904	0.94[CEU][hapmap]
rs4664494	0.88[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs4664497	0.94[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs4664498	0.87[GIH][hapmap]
rs4664501	0.94[CEU][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs5005569	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6433566	0.83[EUR][1000 genomes]
rs6433569	0.88[GIH][hapmap];0.80[JPT][hapmap]
rs6433575	0.94[CEU][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs6711382	0.87[GIH][hapmap]
rs6712443	0.87[GIH][hapmap]
rs6712533	0.87[GIH][hapmap]
rs6713162	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6716286	0.94[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs6729101	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs6730589	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6733811	0.80[JPT][hapmap]
rs6733909	0.94[CEU][hapmap];0.83[GIH][hapmap];0.84[EUR][1000 genomes]
rs6734148	0.94[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap]
rs6735208	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs6760384	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7424335	0.87[GIH][hapmap]
rs7426114	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes]
rs7563441	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs7564024	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7564674	0.83[EUR][1000 genomes]
rs7596744	0.87[CEU][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv469804	chr2:152404429-152570882	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv482520	chr2:152404429-152570882	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9287990	NEB	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152502200-152523000	Weak transcription	Placenta	Placenta
2	chr2:152504400-152531600	Weak transcription	Primary B cells from cord blood	blood
3	chr2:152505200-152543600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:152507600-152521000	Weak transcription	Psoas Muscle	Psoas
5	chr2:152511200-152531200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr2:152511400-152531400	Strong transcription	Fetal Muscle Leg	muscle
7	chr2:152511600-152525800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:152512400-152524400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:152514200-152517600	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:152514600-152542800	Strong transcription	HSMMtube	muscle
11	chr2:152514800-152518000	Weak transcription	K562	blood
12	chr2:152515200-152525400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:152515400-152529000	Weak transcription	Aorta	Aorta
14	chr2:152516600-152521200	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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