Variant report

Variant	rs1853208
Chromosome Location	chr10:96663819-96663820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10882498	0.83[ASN][1000 genomes]
rs11188093	0.83[ASN][1000 genomes]
rs11188105	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11498525	0.82[ASN][1000 genomes]
rs11595422	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1200313	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12772675	0.82[ASN][1000 genomes]
rs12772884	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1322181	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs1341163	0.80[MEX][hapmap]
rs1555474	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap];0.88[YRI][hapmap];0.83[ASN][1000 genomes]
rs1856908	0.82[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs1891071	0.80[MEX][hapmap]
rs1934960	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1934964	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1934965	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1934969	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs1934985	0.80[MEX][hapmap]
rs1998321	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2104161	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs2104162	0.91[ASN][1000 genomes]
rs2253635	0.82[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[ASN][1000 genomes]
rs2275620	0.80[MEX][hapmap]
rs2281889	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.88[YRI][hapmap]
rs2860906	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34234478	0.89[ASN][1000 genomes]
rs35013847	0.92[ASN][1000 genomes]
rs35687798	0.82[ASN][1000 genomes]
rs3740504	0.81[ASN][1000 genomes]
rs4110516	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4362080	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4466755	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4608002	0.91[ASN][1000 genomes]
rs4617515	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs4638239	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4917623	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs4917641	0.82[ASN][1000 genomes]
rs4918758	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4918766	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6583963	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7073165	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7078102	0.84[ASN][1000 genomes]
rs7079343	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7083767	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7084717	0.83[ASN][1000 genomes]
rs7475054	0.86[ASN][1000 genomes]
rs7895223	0.89[ASN][1000 genomes]
rs7895963	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7899661	0.89[ASN][1000 genomes]
rs7910936	0.80[MEX][hapmap]
rs7912502	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7914753	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap]
rs7915414	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7916649	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3344949	chr10:96443874-96666028	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv551955	chr10:96444249-96690371	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1035409	chr10:96495177-96832057	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3529538	chr10:96522848-96700018	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3529539	chr10:96522848-96700018	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3361914	chr10:96522865-96700024	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv523259	chr10:96534584-96693727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv3336672	chr10:96543010-96711519	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1037973	chr10:96563228-96711744	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1047782	chr10:96581094-96718479	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv1818389	chr10:96620304-96675513	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1853208	GOLGA7B	cis	parietal	SCAN
rs1853208	PPP1R3C	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96661800-96665000	Enhancers	Duodenum Mucosa	Duodenum
2	chr10:96662200-96664000	Weak transcription	Fetal Intestine Large	intestine
3	chr10:96662400-96665400	Enhancers	Liver	Liver
4	chr10:96662800-96665200	Enhancers	HepG2	liver
5	chr10:96663000-96664200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:96663000-96665400	Enhancers	Fetal Intestine Small	intestine
7	chr10:96663600-96665600	Enhancers	Stomach Mucosa	stomach
8	chr10:96663800-96664400	Flanking Active TSS	A549	lung

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