Variant report

Variant	rs2119861
Chromosome Location	chr2:187367752-187367753
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	chr2:187366944-187368020	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187365870..187368729-chr2:187369897..187372520,4	K562	blood:
2	chr2:187352868..187356509-chr2:187367066..187369424,5	K562	blood:

Variant related genes	Relation type
ENSG00000268846	TF binding region
ZC3H15	TF binding region
ENSG00000065548	Chromatin interaction
ENSG00000224323	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10194631	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs10200873	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10209563	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs10209572	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs10804005	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10804007	0.83[CHD][hapmap]
rs10931247	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11685403	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11891731	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12693453	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs12997583	0.82[CEU][hapmap]
rs13006571	0.83[CHD][hapmap]
rs1372649	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs1375124	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs1376783	0.81[EUR][1000 genomes]
rs1448854	0.85[TSI][hapmap]
rs1562646	0.85[TSI][hapmap]
rs1584695	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17333648	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17333717	0.80[EUR][1000 genomes]
rs1868384	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1992898	0.83[CHD][hapmap]
rs2044919	0.85[TSI][hapmap]
rs2083678	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2099849	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2119863	0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2197138	0.83[CHD][hapmap]
rs2197787	0.83[CHD][hapmap]
rs2370693	0.83[CHD][hapmap]
rs2887827	0.83[CHD][hapmap]
rs3768776	0.83[TSI][hapmap]
rs3911084	0.83[CHD][hapmap]
rs4144784	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233788	0.83[CHD][hapmap]
rs4365424	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4544390	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4666705	0.85[TSI][hapmap]
rs4666706	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58300265	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6434188	0.91[CHB][hapmap];0.94[CHD][hapmap]
rs66647013	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66694735	0.80[EUR][1000 genomes]
rs6717629	0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6717871	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs6740632	0.85[TSI][hapmap]
rs6741214	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6741369	0.83[CHD][hapmap]
rs6755033	0.80[EUR][1000 genomes]
rs68022965	0.81[EUR][1000 genomes]
rs68161763	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs719071	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs719072	0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs72895450	0.84[EUR][1000 genomes]
rs72897347	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7562659	0.85[TSI][hapmap]
rs7577962	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs7588772	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9333288	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv459988	chr2:187364878-187440683	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv584031	chr2:187364878-187440683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2119861	ZSWIM2	cis	cerebellum	SCAN
rs2119861	ITGAV	cis	cerebellum	SCAN
rs2119861	ITGAV	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187355600-187369000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:187355800-187370200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:187356800-187368400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:187357000-187379000	Strong transcription	Fetal Thymus	thymus
5	chr2:187357400-187383000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:187357600-187382600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:187357600-187386200	Strong transcription	Dnd41	blood
8	chr2:187358200-187379000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:187358600-187379000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:187358600-187385800	Weak transcription	Esophagus	oesophagus
11	chr2:187358800-187367800	Weak transcription	Psoas Muscle	Psoas
12	chr2:187358800-187377200	Strong transcription	HepG2	liver
13	chr2:187359000-187376000	Strong transcription	GM12878-XiMat	blood
14	chr2:187359600-187386400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:187359800-187374800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:187359800-187374800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr2:187359800-187375000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:187359800-187379000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:187359800-187379200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:187359800-187379400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:187359800-187379800	Strong transcription	HSMM	muscle
22	chr2:187359800-187380400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:187359800-187381400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:187359800-187387200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:187360000-187368000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:187360000-187368600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:187360000-187368600	Strong transcription	Adipose Nuclei	Adipose
28	chr2:187360000-187376800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:187360000-187378600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:187360000-187378800	Strong transcription	Liver	Liver
31	chr2:187360000-187379200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:187360000-187386800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:187360200-187368600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:187360200-187369200	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:187360200-187374400	Strong transcription	NH-A	brain
36	chr2:187360200-187374800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr2:187360200-187374800	Strong transcription	Fetal Intestine Large	intestine
38	chr2:187360200-187375400	Strong transcription	Primary B cells from cord blood	blood
39	chr2:187360200-187376800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:187360200-187377000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr2:187360200-187378600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr2:187360200-187379000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr2:187360200-187379200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:187360400-187368800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:187360400-187374800	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:187360800-187368000	Strong transcription	Primary T cells from cord blood	blood
47	chr2:187360800-187368400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:187360800-187369000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:187360800-187374800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:187360800-187379400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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