Variant report

Variant	rs2028016
Chromosome Location	chr7:18834799-18834800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1011446	0.85[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10266741	0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs10280633	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs10950703	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10950704	0.82[JPT][hapmap]
rs12531908	0.81[JPT][hapmap]
rs12533274	0.87[CEU][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12535294	0.94[JPT][hapmap]
rs12539715	0.90[ASN][1000 genomes]
rs12540224	0.88[JPT][hapmap]
rs12540265	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12540872	0.81[JPT][hapmap]
rs12699981	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17349342	0.87[JPT][hapmap]
rs2028012	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2028013	0.92[ASN][1000 genomes]
rs2028014	0.92[ASN][1000 genomes]
rs2073962	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2078866	0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs2078868	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2078869	0.87[JPT][hapmap]
rs2157901	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2257696	0.90[ASN][1000 genomes]
rs2519742	0.91[ASN][1000 genomes]
rs2519744	0.91[ASN][1000 genomes]
rs2519745	0.80[CEU][hapmap];0.92[ASN][1000 genomes]
rs2519746	0.94[JPT][hapmap]
rs2520339	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2520345	0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs2520346	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs2520360	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2588595	0.91[ASN][1000 genomes]
rs2588596	0.90[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2588597	0.94[JPT][hapmap]
rs2588599	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs2588600	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2588601	0.92[ASN][1000 genomes]
rs2588602	0.92[ASN][1000 genomes]
rs2588603	0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs2588604	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2588605	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2588612	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2588623	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2588625	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2588627	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3844320	0.90[ASN][1000 genomes]
rs3852250	0.93[ASN][1000 genomes]
rs3854290	0.93[ASN][1000 genomes]
rs3855596	0.95[ASN][1000 genomes]
rs3901892	0.94[JPT][hapmap]
rs4721725	0.83[CEU][hapmap];0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs62446605	0.87[ASN][1000 genomes]
rs62446608	0.90[ASN][1000 genomes]
rs6461384	0.94[JPT][hapmap]
rs6951973	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6963568	0.88[JPT][hapmap]
rs6972607	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779024	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7779555	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7782894	0.95[ASN][1000 genomes]
rs7783171	0.87[JPT][hapmap]
rs7783209	0.93[ASN][1000 genomes]
rs7785216	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7798677	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7801849	0.95[ASN][1000 genomes]
rs929196	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][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	nsv531368	chr7:18677922-18836920	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv498112	chr7:18677922-18991946	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv887813	chr7:18720135-18995552	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv887814	chr7:18751998-18886177	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2028016	SP8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:18790600-18835000	Weak transcription	Primary B cells from cord blood	blood
2	chr7:18833000-18837200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:18833000-18837800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:18833200-18837800	Weak transcription	NH-A	brain
5	chr7:18833200-18838000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr7:18833400-18837400	Weak transcription	Osteobl	bone
7	chr7:18833400-18838000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:18833400-18838000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:18833400-18838000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:18833800-18835400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:18833800-18835800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:18834000-18838000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:18834200-18845200	Weak transcription	Aorta	Aorta
14	chr7:18834400-18834800	Enhancers	Rectal Smooth Muscle	rectum

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