Variant report

Variant	rs16859632
Chromosome Location	chr3:112193549-112193550
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	chr3:112193285-112195057	GM12878	blood:	n/a	n/a
2	NFATC1	chr3:112193267-112193894	GM12878	blood:	n/a	n/a
3	NFATC1	chr3:112193311-112193938	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112189206..112190998-chr3:112191867..112193876,2	K562	blood:

Variant related genes	Relation type
BTLA	TF binding region
ENSG00000186265	Chromatin interaction

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	0.86[JPT][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]
rs16859629	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	0.86[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[AFR][1000 genomes];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:32 , 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	chr3:112186000-112194400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:112186400-112194400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr3:112186400-112195000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:112186400-112195200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:112186400-112195200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:112188800-112197600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr3:112189200-112193800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:112190600-112194400	Enhancers	Thymus	Thymus
12	chr3:112190600-112198400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr3:112190800-112195400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:112191000-112193600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:112191000-112193800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:112192000-112194200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr3:112192000-112194400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
18	chr3:112192000-112194600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:112192400-112194000	Weak transcription	HepG2	liver
20	chr3:112192400-112194200	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:112192400-112194400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:112192400-112194600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:112192400-112196600	Genic enhancers	Primary B cells from cord blood	blood
24	chr3:112192800-112200200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:112193000-112193600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:112193000-112197800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:112193000-112200000	Weak transcription	Fetal Thymus	thymus
28	chr3:112193200-112193600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:112193200-112201200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:112193400-112193800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:112193400-112194200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:112193400-112195200	Genic enhancers	Primary T cells from cord blood	blood

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