Variant report

Variant	rs16859661
Chromosome Location	chr3:112216360-112216361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 116 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919639	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11921669	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059364	0.96[EUR][1000 genomes]
rs13063173	0.96[EUR][1000 genomes]
rs13064534	0.89[EUR][1000 genomes]
rs13065703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs13070342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs13071492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs13079599	1.00[CEU][hapmap]
rs13080547	0.89[EUR][1000 genomes]
rs13080749	0.96[EUR][1000 genomes]
rs13081201	0.89[EUR][1000 genomes]
rs13081265	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13081632	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13088339	0.89[EUR][1000 genomes]
rs13088349	0.89[EUR][1000 genomes]
rs13088467	0.89[EUR][1000 genomes]
rs13092057	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094161	0.89[EUR][1000 genomes]
rs13094649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs13095000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs13096943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16845067	0.89[EUR][1000 genomes]
rs16859629	0.86[JPT][hapmap]
rs16859632	0.86[JPT][hapmap]
rs16859674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16859727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs16859758	0.96[EUR][1000 genomes]
rs16859775	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16859779	0.89[EUR][1000 genomes]
rs16859787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859793	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859849	1.00[CEU][hapmap]
rs1994711	1.00[JPT][hapmap]
rs2220656	0.89[EUR][1000 genomes]
rs2705526	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28365853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2942062	1.00[JPT][hapmap]
rs34080815	0.96[EUR][1000 genomes]
rs34139211	0.96[EUR][1000 genomes]
rs34248586	0.96[EUR][1000 genomes]
rs34284082	0.85[EUR][1000 genomes]
rs34541731	0.89[EUR][1000 genomes]
rs34596334	0.89[EUR][1000 genomes]
rs34597203	0.96[EUR][1000 genomes]
rs34645913	0.96[EUR][1000 genomes]
rs34829517	0.89[EUR][1000 genomes]
rs34889961	0.96[EUR][1000 genomes]
rs34949685	0.89[EUR][1000 genomes]
rs34962178	0.89[EUR][1000 genomes]
rs35107041	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35240469	0.96[EUR][1000 genomes]
rs35255669	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35349986	0.89[EUR][1000 genomes]
rs35512450	0.96[EUR][1000 genomes]
rs35526995	0.96[EUR][1000 genomes]
rs35529363	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35692417	0.89[EUR][1000 genomes]
rs35709173	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35725070	0.96[EUR][1000 genomes]
rs35748518	0.96[EUR][1000 genomes]
rs35803911	0.89[EUR][1000 genomes]
rs35840933	0.89[EUR][1000 genomes]
rs35931975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs36025914	0.89[EUR][1000 genomes]
rs36031379	0.86[EUR][1000 genomes]
rs36045008	0.89[EUR][1000 genomes]
rs36061184	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36146261	0.89[EUR][1000 genomes]
rs36153507	0.89[EUR][1000 genomes]
rs3736269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs3736270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs3736271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs3773698	0.89[EUR][1000 genomes]
rs3773701	0.89[EUR][1000 genomes]
rs3773704	0.89[EUR][1000 genomes]
rs3773706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs3773710	0.89[EUR][1000 genomes]
rs3821684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs55742760	0.89[EUR][1000 genomes]
rs56662636	0.96[EUR][1000 genomes]
rs56856838	0.96[EUR][1000 genomes]
rs56970524	0.89[EUR][1000 genomes]
rs57346109	0.96[EUR][1000 genomes]
rs58891772	0.96[EUR][1000 genomes]
rs59279185	0.96[EUR][1000 genomes]
rs59858117	0.96[EUR][1000 genomes]
rs60321074	0.89[EUR][1000 genomes]
rs60646325	0.89[EUR][1000 genomes]
rs66486470	0.96[EUR][1000 genomes]
rs66698345	0.85[EUR][1000 genomes]
rs66791711	0.89[EUR][1000 genomes]
rs66910014	0.96[EUR][1000 genomes]
rs67021100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67204151	0.89[EUR][1000 genomes]
rs67513863	0.92[EUR][1000 genomes]
rs67940544	0.89[EUR][1000 genomes]
rs67944354	0.96[EUR][1000 genomes]
rs71317505	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71317506	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317507	0.96[EUR][1000 genomes]
rs71317508	0.96[EUR][1000 genomes]
rs71317510	0.89[EUR][1000 genomes]
rs724125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs73229350	0.96[EUR][1000 genomes]
rs73229353	0.96[EUR][1000 genomes]
rs73229398	0.89[EUR][1000 genomes]
rs958935	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112200600-112217000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:112212600-112216400	Weak transcription	Spleen	Spleen
3	chr3:112212600-112218600	Active TSS	GM12878-XiMat	blood
4	chr3:112213600-112216400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
5	chr3:112214000-112217000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr3:112214000-112218400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:112214400-112218200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:112214600-112218600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr3:112214600-112228600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:112214800-112217600	Active TSS	Thymus	Thymus
11	chr3:112215200-112218000	Active TSS	Fetal Thymus	thymus
12	chr3:112215200-112218600	Active TSS	Primary T cells fromperipheralblood	blood
13	chr3:112215200-112218600	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr3:112215200-112218600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:112215400-112216600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:112215400-112218200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:112215400-112218600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr3:112215600-112216600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:112215600-112218400	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:112215600-112218400	Active TSS	Small Intestine	intestine
21	chr3:112215800-112217200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr3:112215800-112217800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr3:112215800-112218800	Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr3:112216000-112216600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
25	chr3:112216000-112216600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:112216200-112216400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:112216200-112216600	Active TSS	Primary hematopoietic stem cells	blood
28	chr3:112216200-112216600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:112216200-112217200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr3:112216200-112218800	Active TSS	Primary T killer memory cells from peripheral blood	blood

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