Variant report

Variant	rs11688988
Chromosome Location	chr2:187292414-187292415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10169008	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169206	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177153	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190003	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196955	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198525	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200749	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205170	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10208643	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497671	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931240	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11675633	0.89[ASN][1000 genomes]
rs11690758	0.89[ASN][1000 genomes]
rs11692347	0.89[ASN][1000 genomes]
rs11888880	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11888881	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11901465	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11903027	0.89[ASN][1000 genomes]
rs12328822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392819	0.89[ASN][1000 genomes]
rs13397188	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398352	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13414850	0.89[ASN][1000 genomes]
rs13428033	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1448848	0.89[ASN][1000 genomes]
rs1448855	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448857	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1868383	0.89[ASN][1000 genomes]
rs2084488	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2084489	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084490	0.84[ASN][1000 genomes]
rs2197139	0.89[ASN][1000 genomes]
rs2370688	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2887826	0.89[ASN][1000 genomes]
rs34234405	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642346	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56137171	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61434493	0.89[ASN][1000 genomes]
rs6434174	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6710436	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715493	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717505	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6721789	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728382	0.89[ASN][1000 genomes]
rs6728400	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6744717	0.89[ASN][1000 genomes]
rs72895449	0.89[ASN][1000 genomes]
rs7579259	0.89[ASN][1000 genomes]
rs7582412	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584137	0.89[ASN][1000 genomes]
rs7585905	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597954	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606920	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9288129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917285	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1005680	chr2:187244500-187320653	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536080	chr2:187244500-187320653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1001927	chr2:187264940-187325667	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv997835	chr2:187265730-187327561	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv536081	chr2:187265730-187327561	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11688988	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187274200-187294000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:187276200-187293000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:187279800-187300600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:187281600-187292800	Weak transcription	Liver	Liver
5	chr2:187282400-187299200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:187287200-187300800	Weak transcription	Ovary	ovary
7	chr2:187287400-187298000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:187287600-187292600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:187287800-187293200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:187288600-187301200	Weak transcription	Gastric	stomach
11	chr2:187289200-187300800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:187290000-187293000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:187290200-187298200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr2:187290600-187304200	Weak transcription	Stomach Mucosa	stomach
15	chr2:187291400-187296600	Weak transcription	Fetal Stomach	stomach
16	chr2:187291600-187296400	Weak transcription	Fetal Intestine Small	intestine
17	chr2:187291600-187298800	Weak transcription	Fetal Intestine Large	intestine
18	chr2:187291800-187292800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:187291800-187292800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:187291800-187292800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:187291800-187299200	Weak transcription	Primary B cells from cord blood	blood
22	chr2:187291800-187300400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:187291800-187301800	Weak transcription	GM12878-XiMat	blood
24	chr2:187292000-187298400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:187292000-187301200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:187292400-187292600	Enhancers	Dnd41	blood
27	chr2:187292400-187293000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr2:187292400-187293200	Enhancers	HepG2	liver
29	chr2:187292400-187293800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:187292400-187299000	Weak transcription	Primary T cells from cord blood	blood
31	chr2:187292400-187299000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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