Variant report

Variant	rs2705565
Chromosome Location	chr3:112219336-112219337
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	chr3:112219336-112220020	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112215809..112217939-chr3:112219323..112221326,2	K562	blood:

Variant related genes	Relation type
BTLA	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1105938	0.86[ASN][1000 genomes]
rs1155073	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12632867	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs1386895	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.90[EUR][1000 genomes]
rs1398091	1.00[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs1488259	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1512006	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs1533159	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs1601852	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1814052	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1844089	0.81[CHB][hapmap]
rs1873571	0.81[CHB][hapmap]
rs1873572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1877363	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs2137199	0.83[EUR][1000 genomes]
rs2171513	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap]
rs2171514	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292442	0.86[ASN][1000 genomes]
rs2633556	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2633557	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2633560	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2633562	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2633563	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2633574	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2633575	0.94[ASN][1000 genomes]
rs2633578	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs2633579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633580	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs2633582	0.81[CHB][hapmap]
rs2633588	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2633589	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2638013	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2638015	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2638016	0.81[CHB][hapmap]
rs2638017	0.81[CHB][hapmap]
rs2638019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2638022	0.81[CHB][hapmap]
rs2638023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2638026	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs2638028	0.86[ASN][1000 genomes]
rs2638029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs2638031	0.81[CHB][hapmap]
rs2638032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2638035	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2638037	0.81[CHB][hapmap]
rs2638039	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[ASN][1000 genomes]
rs2668219	0.86[ASN][1000 genomes]
rs2705505	0.87[ASN][1000 genomes]
rs2705507	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2705515	0.86[ASN][1000 genomes]
rs2705518	0.86[ASN][1000 genomes]
rs2705519	0.89[ASN][1000 genomes]
rs2705521	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs2705522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs2705525	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2705533	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2705534	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs2705535	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2705536	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2705541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2705544	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs2705548	0.96[ASN][1000 genomes]
rs2705552	0.96[ASN][1000 genomes]
rs2705555	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2705556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs2705559	0.81[CHB][hapmap]
rs2705560	0.86[ASN][1000 genomes]
rs2705562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs2705564	0.86[ASN][1000 genomes]
rs2705566	0.85[CHB][hapmap]
rs2933134	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs2933135	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs2933137	0.84[ASN][1000 genomes]
rs2942061	0.86[ASN][1000 genomes]
rs2952319	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs2952320	0.86[ASN][1000 genomes]
rs2952323	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs2952324	0.94[ASN][1000 genomes]
rs2952325	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2952326	0.81[CHB][hapmap]
rs2952327	0.81[CHB][hapmap]
rs2969895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2969896	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs2971204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112268	1.00[ASN][1000 genomes]
rs4519670	0.83[EUR][1000 genomes]
rs4682410	0.82[CEU][hapmap];0.91[GIH][hapmap];0.90[EUR][1000 genomes]
rs6438079	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[EUR][1000 genomes]
rs6792947	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs728568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]
rs751875	0.86[ASN][1000 genomes]
rs7652377	0.82[CEU][hapmap]
rs766968	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs766969	0.86[ASN][1000 genomes]
rs9288952	0.82[CEU][hapmap]
rs9848054	0.82[CEU][hapmap]
rs9866734	0.82[CEU][hapmap]
rs9869455	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9869579	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs998036	0.88[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2705565	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112214600-112228600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112218400-112220000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:112218400-112220600	Enhancers	HUVEC	blood vessel
4	chr3:112218600-112222400	Weak transcription	Fetal Thymus	thymus
5	chr3:112218800-112219400	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr3:112218800-112219400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr3:112218800-112219800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:112218800-112219800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr3:112218800-112220800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:112218800-112222800	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:112218800-112241600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr3:112219000-112219800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:112219000-112219800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:112219000-112219800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:112219000-112225000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:112219200-112219600	Enhancers	Primary B cells from cord blood	blood
17	chr3:112219200-112219600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:112219200-112219600	Enhancers	GM12878-XiMat	blood

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