Variant report

Variant	rs11690758
Chromosome Location	chr2:187370673-187370674
allele	C/G
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	chr2:187368474-187377795	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:187368558-187372687	K562	blood:	n/a	n/a
3	POLR2A	chr2:187370630-187370677	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:187370417-187370716	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:187365870..187368729-chr2:187369897..187372520,4	K562	blood:
2	chr2:187370609..187373386-chr2:187454442..187456199,2	MCF-7	breast:
3	chr2:187370485..187373217-chr2:187453776..187456177,3	MCF-7	breast:

Variant related genes	Relation type
ZC3H15	TF binding region
ENSG00000268846	TF binding region
ENSG00000138448	Chromatin interaction
ENSG00000268846	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10178888	0.85[EUR][1000 genomes]
rs10181681	0.80[EUR][1000 genomes]
rs10190003	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10196955	0.89[ASN][1000 genomes]
rs10198525	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10200749	0.85[ASN][1000 genomes]
rs10208643	0.89[ASN][1000 genomes]
rs1037241	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497671	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11675633	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675656	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11678950	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11680486	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688988	0.89[ASN][1000 genomes]
rs11692028	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693797	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11888432	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11895483	0.82[EUR][1000 genomes]
rs11898666	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11901465	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328822	0.89[ASN][1000 genomes]
rs13392819	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393891	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13394241	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13397188	0.89[ASN][1000 genomes]
rs13401304	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13428033	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448848	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448849	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16827968	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16827994	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1868383	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869031	0.83[EUR][1000 genomes]
rs2044683	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2084488	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084489	0.89[ASN][1000 genomes]
rs2084490	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2197139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370688	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887826	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642346	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719959	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56137171	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61226319	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61434493	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434167	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6709401	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6716324	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717525	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721789	0.89[ASN][1000 genomes]
rs6724161	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6728382	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731567	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6744717	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72893450	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72895449	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72897386	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72901315	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72901322	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7579259	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585889	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588607	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597954	0.89[ASN][1000 genomes]
rs7603088	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9288129	0.89[ASN][1000 genomes]
rs9917285	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11690758	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187357000-187379000	Strong transcription	Fetal Thymus	thymus
2	chr2:187357400-187383000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:187357600-187382600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:187357600-187386200	Strong transcription	Dnd41	blood
5	chr2:187358200-187379000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr2:187358600-187379000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:187358600-187385800	Weak transcription	Esophagus	oesophagus
8	chr2:187358800-187377200	Strong transcription	HepG2	liver
9	chr2:187359000-187376000	Strong transcription	GM12878-XiMat	blood
10	chr2:187359600-187386400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:187359800-187374800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:187359800-187374800	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:187359800-187375000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:187359800-187379000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:187359800-187379200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:187359800-187379400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:187359800-187379800	Strong transcription	HSMM	muscle
18	chr2:187359800-187380400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:187359800-187381400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:187359800-187387200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:187360000-187376800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:187360000-187378600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:187360000-187378800	Strong transcription	Liver	Liver
24	chr2:187360000-187379200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:187360000-187386800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:187360200-187374400	Strong transcription	NH-A	brain
27	chr2:187360200-187374800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr2:187360200-187374800	Strong transcription	Fetal Intestine Large	intestine
29	chr2:187360200-187375400	Strong transcription	Primary B cells from cord blood	blood
30	chr2:187360200-187376800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:187360200-187377000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:187360200-187378600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:187360200-187379000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr2:187360200-187379200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:187360400-187374800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr2:187360800-187374800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:187360800-187379400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:187361200-187385600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:187361400-187376800	Strong transcription	Osteobl	bone
40	chr2:187361400-187389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:187361800-187377800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:187362200-187378400	Strong transcription	K562	blood
43	chr2:187362400-187375800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:187363000-187374400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:187363000-187375200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:187363000-187385600	Weak transcription	Aorta	Aorta
47	chr2:187363000-187387800	Weak transcription	Pancreas	Pancrea
48	chr2:187363000-187408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:187363200-187397600	Weak transcription	Small Intestine	intestine
50	chr2:187363600-187378600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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