Variant report

Variant	rs11919639
Chromosome Location	chr3:112208750-112208751
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10511317	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11921669	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13059364	0.89[EUR][1000 genomes]
rs13063173	0.89[EUR][1000 genomes]
rs13064534	0.83[EUR][1000 genomes]
rs13065703	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13070342	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13071492	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13079599	1.00[CEU][hapmap]
rs13080547	0.82[EUR][1000 genomes]
rs13080749	0.89[EUR][1000 genomes]
rs13081201	0.82[EUR][1000 genomes]
rs13081265	0.93[EUR][1000 genomes]
rs13081632	0.93[EUR][1000 genomes]
rs13088339	0.82[EUR][1000 genomes]
rs13088349	0.82[EUR][1000 genomes]
rs13088467	0.82[EUR][1000 genomes]
rs13092057	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13094161	0.82[EUR][1000 genomes]
rs13094649	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13095000	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13096943	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16845067	0.82[EUR][1000 genomes]
rs16859629	0.85[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs16859632	0.86[JPT][hapmap]
rs16859661	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16859674	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16859727	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs16859758	0.89[EUR][1000 genomes]
rs16859775	0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16859779	0.82[EUR][1000 genomes]
rs16859787	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16859793	0.82[EUR][1000 genomes]
rs16859849	1.00[CEU][hapmap]
rs1994711	1.00[JPT][hapmap]
rs2220656	0.82[EUR][1000 genomes]
rs2705526	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28365853	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2942062	1.00[JPT][hapmap]
rs34080815	0.89[EUR][1000 genomes]
rs34139211	0.89[EUR][1000 genomes]
rs34248586	0.89[EUR][1000 genomes]
rs34541731	0.82[EUR][1000 genomes]
rs34596334	0.82[EUR][1000 genomes]
rs34597203	0.89[EUR][1000 genomes]
rs34645913	0.89[EUR][1000 genomes]
rs34829517	0.82[EUR][1000 genomes]
rs34889961	0.89[EUR][1000 genomes]
rs34949685	0.82[EUR][1000 genomes]
rs34962178	0.82[EUR][1000 genomes]
rs35107041	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35240469	0.89[EUR][1000 genomes]
rs35255669	0.82[EUR][1000 genomes]
rs35349986	0.82[EUR][1000 genomes]
rs35512450	0.89[EUR][1000 genomes]
rs35526995	0.89[EUR][1000 genomes]
rs35529363	0.82[EUR][1000 genomes]
rs35692417	0.82[EUR][1000 genomes]
rs35709173	0.82[EUR][1000 genomes]
rs35725070	0.89[EUR][1000 genomes]
rs35748518	0.89[EUR][1000 genomes]
rs35803911	0.82[EUR][1000 genomes]
rs35840933	0.82[EUR][1000 genomes]
rs35931975	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs36025914	0.82[EUR][1000 genomes]
rs36045008	0.82[EUR][1000 genomes]
rs36061184	0.82[EUR][1000 genomes]
rs36146261	0.82[EUR][1000 genomes]
rs36153507	0.82[EUR][1000 genomes]
rs3736269	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3736270	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3736271	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3773698	0.82[EUR][1000 genomes]
rs3773701	0.82[EUR][1000 genomes]
rs3773704	0.82[EUR][1000 genomes]
rs3773706	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs3773710	0.82[EUR][1000 genomes]
rs3821684	1.00[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs55742760	0.82[EUR][1000 genomes]
rs56662636	0.89[EUR][1000 genomes]
rs56856838	0.89[EUR][1000 genomes]
rs56970524	0.82[EUR][1000 genomes]
rs57346109	0.89[EUR][1000 genomes]
rs58891772	0.89[EUR][1000 genomes]
rs59279185	0.89[EUR][1000 genomes]
rs59858117	0.89[EUR][1000 genomes]
rs60321074	0.82[EUR][1000 genomes]
rs60646325	0.82[EUR][1000 genomes]
rs6438081	1.00[GIH][hapmap]
rs66486470	0.89[EUR][1000 genomes]
rs66698345	0.86[EUR][1000 genomes]
rs66791711	0.82[EUR][1000 genomes]
rs66910014	0.89[EUR][1000 genomes]
rs67021100	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67204151	0.82[EUR][1000 genomes]
rs67513863	0.85[EUR][1000 genomes]
rs67940544	0.82[EUR][1000 genomes]
rs67944354	0.89[EUR][1000 genomes]
rs71317505	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71317506	0.93[EUR][1000 genomes]
rs71317507	0.89[EUR][1000 genomes]
rs71317508	0.89[EUR][1000 genomes]
rs71317510	0.82[EUR][1000 genomes]
rs724125	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs73229350	0.89[EUR][1000 genomes]
rs73229353	0.89[EUR][1000 genomes]
rs73229398	0.82[EUR][1000 genomes]
rs7612986	0.94[AFR][1000 genomes]
rs958935	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[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
rs11919639	SLC35A5	cis	multi-tissue	Pritchard
rs11919639	SLC35A5	cis	Thyroid	GTEx
rs11919639	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:22 , 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	chr3:112200600-112217000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:112201400-112215600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:112202400-112208800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:112206400-112210400	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr3:112206400-112214000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:112206800-112209000	Genic enhancers	Primary B cells from cord blood	blood
9	chr3:112207600-112209800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:112207800-112214000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:112207800-112214000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:112208000-112208800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
13	chr3:112208000-112209400	Enhancers	Primary T cells from cord blood	blood
14	chr3:112208400-112208800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
15	chr3:112208600-112208800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:112208600-112208800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:112208600-112208800	Enhancers	Thymus	Thymus
18	chr3:112208600-112209000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:112208600-112211000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr3:112208600-112212600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr3:112208600-112212600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr3:112208600-112212600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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