Variant report

Variant	rs6438079
Chromosome Location	chr3:112196075-112196076
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12632867	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1386895	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1398091	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[EUR][1000 genomes]
rs1512006	0.88[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap]
rs1814052	0.90[EUR][1000 genomes]
rs1844089	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs1873571	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs1877363	0.88[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap]
rs2171513	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs2171514	0.87[EUR][1000 genomes]
rs2633555	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2633556	0.87[EUR][1000 genomes]
rs2633557	0.97[EUR][1000 genomes]
rs2633560	0.97[EUR][1000 genomes]
rs2633562	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs2633563	0.93[EUR][1000 genomes]
rs2633578	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]
rs2633579	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2633580	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]
rs2633582	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2633584	0.80[AMR][1000 genomes]
rs2633588	0.90[EUR][1000 genomes]
rs2633589	0.90[EUR][1000 genomes]
rs2638013	0.90[EUR][1000 genomes]
rs2638015	0.87[EUR][1000 genomes]
rs2638016	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2638017	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2638022	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs2638031	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs2638037	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs2638039	0.83[CHB][hapmap]
rs2705517	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2705525	0.90[EUR][1000 genomes]
rs2705531	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2705532	0.82[ASN][1000 genomes]
rs2705533	0.90[EUR][1000 genomes]
rs2705534	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]
rs2705536	0.90[EUR][1000 genomes]
rs2705544	1.00[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2705555	0.97[EUR][1000 genomes]
rs2705559	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2705565	1.00[CEU][hapmap];0.91[GIH][hapmap];0.90[EUR][1000 genomes]
rs2705566	0.93[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs2952323	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2952326	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2952327	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2971204	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4519670	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682410	0.94[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6774355	0.85[AMR][1000 genomes]
rs6792947	0.88[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap]
rs7652377	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs766968	0.88[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap]
rs9288952	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9756562	0.80[AMR][1000 genomes]
rs9848054	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs9854043	0.82[AMR][1000 genomes]
rs9854311	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9866734	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs9869455	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs9869579	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6438079	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112188800-112197600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr3:112190600-112198400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:112192400-112196600	Genic enhancers	Primary B cells from cord blood	blood
4	chr3:112192800-112200200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112193000-112197800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:112193000-112200000	Weak transcription	Fetal Thymus	thymus
7	chr3:112193200-112201200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:112193800-112197000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:112194200-112196400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:112194200-112214000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:112194400-112196600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:112194400-112197000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:112194400-112198200	Weak transcription	Thymus	Thymus
14	chr3:112194400-112199800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:112194600-112197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:112194600-112199800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:112195000-112198000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:112195200-112196200	Strong transcription	Primary T cells from cord blood	blood
19	chr3:112195200-112196400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:112195200-112197000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:112195200-112198200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:112195400-112197000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:112195400-112200800	ZNF genes & repeats	GM12878-XiMat	blood
24	chr3:112195600-112196600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:112195800-112197200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:112195800-112198200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:112196000-112197400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr3:112196000-112198000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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