Variant report

Variant	rs16859629
Chromosome Location	chr3:112190380-112190381
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	chr3:112188609-112190411	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
BTLA	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10511317	0.86[JPT][hapmap]
rs11919639	0.85[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs13065703	0.86[JPT][hapmap]
rs13070342	0.86[JPT][hapmap]
rs13071492	0.86[JPT][hapmap]
rs13094649	0.86[JPT][hapmap]
rs13095000	0.86[JPT][hapmap]
rs16859632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16859661	0.86[JPT][hapmap]
rs16859674	0.86[JPT][hapmap]
rs16859727	0.86[JPT][hapmap]
rs16859775	0.86[JPT][hapmap]
rs16859787	0.86[JPT][hapmap]
rs1994711	0.86[JPT][hapmap]
rs28365853	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs2942062	0.86[JPT][hapmap]
rs35931975	0.86[JPT][hapmap]
rs3736269	0.86[JPT][hapmap]
rs3736270	0.86[JPT][hapmap]
rs3736271	0.86[JPT][hapmap]
rs3773706	0.86[JPT][hapmap]
rs3821684	0.86[JPT][hapmap]
rs60551879	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs724125	0.86[JPT][hapmap]
rs958935	0.86[JPT][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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112180400-112195400	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr3:112182200-112193600	Weak transcription	Spleen	Spleen
3	chr3:112183800-112195000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr3:112184200-112190600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:112184200-112191600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:112185000-112190600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:112185000-112190600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:112185200-112190400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:112185400-112190400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:112185400-112192200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:112186000-112194400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:112186400-112192000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:112186400-112194400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:112186400-112195000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:112186400-112195200	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr3:112186400-112195200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:112186800-112190400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:112186800-112191800	Genic enhancers	Primary B cells from cord blood	blood
19	chr3:112187000-112190600	Weak transcription	Thymus	Thymus
20	chr3:112188000-112192000	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:112188400-112190600	Genic enhancers	Primary T cells from cord blood	blood
22	chr3:112188600-112190800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:112188600-112191000	Enhancers	Osteobl	bone
24	chr3:112188600-112192200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:112188600-112192400	Enhancers	HSMM	muscle
26	chr3:112188800-112190400	Enhancers	HSMMtube	muscle
27	chr3:112188800-112190800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:112188800-112190800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:112188800-112191000	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr3:112188800-112191200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:112188800-112191200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:112188800-112197600	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr3:112189000-112192000	Genic enhancers	GM12878-XiMat	blood
34	chr3:112189200-112190400	Enhancers	Aorta	Aorta
35	chr3:112189200-112190800	Weak transcription	Adipose Nuclei	Adipose
36	chr3:112189200-112193800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:112189400-112191200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:112189600-112190600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:112189600-112192600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:112189800-112191000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:112189800-112193000	Enhancers	Fetal Thymus	thymus
42	chr3:112190000-112190400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:112190000-112190600	Enhancers	Fetal Lung	lung
44	chr3:112190000-112192000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:112190200-112190400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:112190200-112190800	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links