Variant report

Variant	rs2671699
Chromosome Location	chr10:50127053-50127054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:50126972-50127069	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
LRRC18	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10735227	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10745285	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10745287	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10745288	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10745289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776655	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776656	1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776657	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857659	1.00[CHB][hapmap]
rs11101568	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1317894	1.00[CHB][hapmap]
rs17011795	1.00[CHB][hapmap]
rs1913524	1.00[CHB][hapmap]
rs2137921	1.00[CHB][hapmap]
rs2244085	1.00[CHB][hapmap]
rs2244704	1.00[CHB][hapmap]
rs2244777	1.00[CHB][hapmap]
rs2252692	1.00[CHB][hapmap]
rs2377632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377649	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377694	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2458674	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][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];1.00[ASN][1000 genomes]
rs2466750	1.00[CHB][hapmap]
rs2663018	1.00[CHB][hapmap]
rs2663024	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2663027	1.00[CHB][hapmap]
rs2663058	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663061	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2663062	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2671698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2671700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2671701	1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2889691	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940718	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940723	1.00[ASN][1000 genomes]
rs2943248	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750866	1.00[CHB][hapmap]
rs3810953	1.00[CHB][hapmap]
rs3849151	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838432	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61848099	1.00[ASN][1000 genomes]
rs61848100	1.00[ASN][1000 genomes]
rs7080003	1.00[CHB][hapmap]
rs7094724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7905794	1.00[CHB][hapmap]
rs7911009	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv517287	chr10:50122181-50134266	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2671699	SYT15	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50074600-50129600	Strong transcription	Primary B cells from cord blood	blood
2	chr10:50109400-50127800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr10:50121000-50134800	Weak transcription	Spleen	Spleen
4	chr10:50121000-50155800	Weak transcription	Primary T cells from cord blood	blood
5	chr10:50124400-50127600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:50124800-50131800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr10:50124800-50134400	Weak transcription	GM12878-XiMat	blood
8	chr10:50125400-50154400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:50126000-50127400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:50126000-50127400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:50126000-50133000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr10:50126000-50133400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr10:50126200-50130200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr10:50126400-50127400	Weak transcription	Small Intestine	intestine

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