Variant report

Variant	rs2359661
Chromosome Location	chr16:31281147-31281148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr16:31280658-31281401	MCF-7	breast:	n/a	n/a
2	CTCF	chr16:31281080-31281230	GM12873	blood:	n/a	n/a
3	SIN3AK20	chr16:31280621-31281238	MCF-7	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31278411..31282963-chr16:31285984..31289052,5	MCF-7	breast:
2	chr16:31225508..31229530-chr16:31277117..31281279,6	MCF-7	breast:
3	chr16:31225327..31230953-chr16:31277531..31282411,8	MCF-7	breast:
4	chr16:31272641..31274677-chr16:31278876..31282230,3	MCF-7	breast:
5	chr16:31276981..31278579-chr16:31279607..31281902,2	MCF-7	breast:
6	chr16:31278987..31281601-chr16:31282208..31284163,2	MCF-7	breast:
7	chr16:31190241..31193452-chr16:31279543..31282483,4	MCF-7	breast:
8	chr16:31279444..31281595-chr16:31287575..31289150,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU7-199P	TF binding region
ITGAM	TF binding region
ENSG00000177238	Chromatin interaction
ENSG00000169896	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000169900	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10438639	0.85[ASN][1000 genomes]
rs10782004	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs1106398	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11150608	0.87[ASN][1000 genomes]
rs11150610	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs11150612	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs11150613	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs11150614	0.85[CHB][hapmap]
rs11150616	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1143682	0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs11574630	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs11574631	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs11641202	0.94[ASW][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs11641624	0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs11645526	0.84[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs11865830	0.85[ASN][1000 genomes]
rs12598380	0.92[ASN][1000 genomes]
rs12923297	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs13332545	0.84[JPT][hapmap]
rs1808430	0.81[ASN][1000 genomes]
rs2011491	0.99[ASN][1000 genomes]
rs3087796	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs3764327	0.84[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs3815801	0.81[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs4077810	0.93[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs4447446	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459557	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs4506917	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap]
rs4561481	0.84[ASN][1000 genomes]
rs4597342	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4889639	0.82[ASN][1000 genomes]
rs4889640	0.92[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs4889644	0.85[ASN][1000 genomes]
rs4889649	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs60660286	0.82[ASN][1000 genomes]
rs6565225	0.99[ASN][1000 genomes]
rs7193943	0.84[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs7196256	0.85[ASN][1000 genomes]
rs7206295	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7499192	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8048583	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8051304	0.84[ASN][1000 genomes]
rs8057320	0.84[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs8060268	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs8062426	0.84[ASN][1000 genomes]
rs889549	0.84[ASN][1000 genomes]
rs889551	0.84[ASN][1000 genomes]
rs929868	0.99[ASN][1000 genomes]
rs9673519	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9923270	0.81[ASN][1000 genomes]
rs9938177	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2359661	PYCARD	cis	lymphoblastoid	seeQTL
rs2359661	RABEP2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31277200-31283200	Weak transcription	Lung	lung
2	chr16:31277400-31284600	Weak transcription	HMEC	breast
3	chr16:31277400-31289000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr16:31277400-31290000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr16:31277600-31283200	Weak transcription	Spleen	Spleen
6	chr16:31277600-31284800	Weak transcription	Primary B cells from cord blood	blood
7	chr16:31277600-31285000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr16:31277600-31290400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr16:31277600-31290400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr16:31277600-31290600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr16:31277800-31284800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr16:31278000-31286600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr16:31279200-31284800	Weak transcription	NHEK	skin
14	chr16:31279600-31288600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:31279600-31290400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr16:31280000-31281400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr16:31280000-31288200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr16:31280200-31281200	Strong transcription	Primary B cells from peripheral blood	blood
19	chr16:31280400-31281400	Enhancers	A549	lung
20	chr16:31280600-31282000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr16:31281000-31281400	Enhancers	GM12878-XiMat	blood
22	chr16:31281000-31282400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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