Variant report

Variant	rs1935474
Chromosome Location	chr10:56099530-56099531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10825295	0.83[CHB][hapmap]
rs11004208	0.87[ASN][1000 genomes]
rs11004223	0.84[CHB][hapmap]
rs11004230	0.84[CHB][hapmap]
rs11591584	0.83[CHB][hapmap]
rs11592872	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs11594789	0.82[CHB][hapmap]
rs1159864	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12241144	0.84[CHB][hapmap]
rs12242118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12247773	0.81[CHB][hapmap]
rs12255969	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12256455	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs12262364	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs12571998	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1342287	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1342289	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1342291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342303	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap]
rs1342304	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1361712	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs1561670	0.84[CHB][hapmap]
rs1578667	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1578668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1592178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16905888	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs16905927	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2043997	0.84[CHB][hapmap]
rs2043998	0.84[CHB][hapmap]
rs2043999	0.84[CHB][hapmap]
rs2044002	0.84[CHB][hapmap]
rs2096173	0.86[ASN][1000 genomes]
rs2153821	0.86[CEU][hapmap]
rs2153822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2583021	0.90[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2583024	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs2583030	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[YRI][hapmap]
rs2795923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795924	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795927	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2795929	0.85[CEU][hapmap]
rs2795930	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs6481088	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7067767	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7077543	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs7080899	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73243269	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7901023	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7906254	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs7914488	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs7921798	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs966910	0.84[CHB][hapmap]
rs997064	0.84[CHB][hapmap]
rs997065	0.84[CHB][hapmap]
rs997066	0.84[CHB][hapmap]
rs997067	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054364	chr10:55925471-56196447	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv540633	chr10:55925471-56196447	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2753511	chr10:56022197-56153636	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1044020	chr10:56038546-56224736	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv540634	chr10:56038546-56224736	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1048014	chr10:56053413-56104109	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv831879	chr10:56059973-56210729	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv467217	chr10:56072949-56104585	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
9	nsv550952	chr10:56072949-56104585	Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
10	nsv1052386	chr10:56075990-56273476	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv895434	chr10:56076004-56119975	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
12	nsv895435	chr10:56076975-56108631	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
13	nsv895436	chr10:56076975-56114857	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
14	nsv895437	chr10:56083891-56132046	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
15	nsv895438	chr10:56083891-56146761	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
16	nsv550953	chr10:56084933-56126202	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
17	nsv467218	chr10:56084933-56132046	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
18	nsv550954	chr10:56084933-56132046	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
19	nsv550955	chr10:56084933-56146761	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
20	nsv895439	chr10:56084933-56146761	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
21	nsv467219	chr10:56087423-56126202	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
22	nsv550956	chr10:56087423-56126202	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1935474	MBL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:56098600-56101000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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