Variant report

Variant	rs2705534
Chromosome Location	chr3:112208385-112208386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs11706550	0.89[EUR][1000 genomes]
rs12632867	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs1386895	0.83[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1398091	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs1512005	0.89[EUR][1000 genomes]
rs1512006	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1533159	0.81[CHB][hapmap]
rs1844089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1873571	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs1873572	0.81[CHB][hapmap]
rs1877363	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1994713	0.89[EUR][1000 genomes]
rs2131008	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2171513	0.81[CHB][hapmap]
rs2279532	0.89[EUR][1000 genomes]
rs2280066	0.89[EUR][1000 genomes]
rs2633555	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2633562	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs2633574	0.81[CHB][hapmap]
rs2633578	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2633579	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2633580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2633582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2633584	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2638016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2638017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2638018	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2638019	0.81[CHB][hapmap]
rs2638022	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2638023	0.81[CHB][hapmap]
rs2638026	0.81[CHB][hapmap]
rs2638029	0.81[CHB][hapmap]
rs2638031	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs2638032	0.81[CHB][hapmap]
rs2638035	0.81[CHB][hapmap]
rs2638037	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2638039	0.91[CHB][hapmap]
rs2638042	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2638045	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2705507	0.81[CHB][hapmap]
rs2705517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2705521	0.81[CHB][hapmap]
rs2705522	0.81[CHB][hapmap]
rs2705531	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2705532	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705541	0.81[CHB][hapmap]
rs2705544	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2705556	0.81[CHB][hapmap]
rs2705559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2705562	0.81[CHB][hapmap]
rs2705565	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs2705566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28866814	0.89[EUR][1000 genomes]
rs2933134	0.81[CHB][hapmap]
rs2933135	0.81[CHB][hapmap]
rs2933142	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2952319	0.81[CHB][hapmap]
rs2952323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2952326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2952327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2969895	0.80[CHB][hapmap]
rs2969896	0.81[CHB][hapmap]
rs2971204	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs34233684	0.89[EUR][1000 genomes]
rs3732815	0.89[EUR][1000 genomes]
rs4519670	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4682410	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4682413	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs5000995	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6438079	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6774355	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6792947	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs728568	0.81[CHB][hapmap]
rs7625366	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7652377	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs766968	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs9288952	0.88[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs9288954	0.89[EUR][1000 genomes]
rs9756562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9809247	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9848054	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9854043	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866734	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs9869455	0.85[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs9869579	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS 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	28 gene(s)	inside rSNPs	diseases
9	nsv963487	chr3:112204269-112213816	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2705534	SLC35A5	cis	lymphoblastoid	seeQTL
rs2705534	SLC35A5	cis	Lymphoblastoid	GTEx
rs2705534	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112194200-112214000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:112200400-112214800	Weak transcription	Fetal Thymus	thymus
3	chr3:112200600-112208600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr3:112200600-112217000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112201400-112208600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:112201400-112215600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:112201800-112208600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:112202200-112208600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:112202400-112208800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:112202600-112208600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr3:112206400-112210400	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr3:112206400-112214000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr3:112206600-112208600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:112206800-112209000	Genic enhancers	Primary B cells from cord blood	blood
15	chr3:112207000-112208400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr3:112207600-112209800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:112207800-112214000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:112207800-112214000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:112208000-112208800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
20	chr3:112208000-112209400	Enhancers	Primary T cells from cord blood	blood

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