Variant report

Variant	rs11925823
Chromosome Location	chr3:47443065-47443066
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47434735..47437692-chr3:47441632..47443336,2	MCF-7	breast:
2	chr3:47423869..47425978-chr3:47441656..47444550,3	K562	blood:
3	chr3:47422123..47424705-chr3:47440996..47443292,2	K562	blood:

Variant related genes	Relation type
ENSG00000260236	Chromatin interaction
ENSG00000076201	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1038394	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10865946	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130127	0.88[EUR][1000 genomes]
rs11130128	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130129	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130132	0.82[EUR][1000 genomes]
rs11705957	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711824	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11712445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716763	0.85[EUR][1000 genomes]
rs11719877	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11914932	0.80[EUR][1000 genomes]
rs11927371	0.84[EUR][1000 genomes]
rs12486969	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487736	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12489046	0.86[EUR][1000 genomes]
rs12490058	0.82[EUR][1000 genomes]
rs12492433	0.86[EUR][1000 genomes]
rs12497225	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12630641	0.80[EUR][1000 genomes]
rs12632132	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12636851	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13059519	0.81[EUR][1000 genomes]
rs13064843	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13075233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13079098	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531875	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17411375	0.88[EUR][1000 genomes]
rs17784882	0.82[EUR][1000 genomes]
rs1872164	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2062278	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2101247	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2159400	0.87[EUR][1000 genomes]
rs2291298	0.80[EUR][1000 genomes]
rs295428	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs295449	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs295458	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs295461	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3736177	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816779	0.80[EUR][1000 genomes]
rs4241548	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858805	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858848	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858868	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858888	0.88[EUR][1000 genomes]
rs4858890	0.82[EUR][1000 genomes]
rs4858894	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs553989	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56032309	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56351005	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57346147	0.99[EUR][1000 genomes]
rs59586735	0.85[EUR][1000 genomes]
rs60369822	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62246474	0.88[EUR][1000 genomes]
rs62248580	0.90[EUR][1000 genomes]
rs62248599	0.84[EUR][1000 genomes]
rs6765990	0.81[EUR][1000 genomes]
rs6780013	0.88[EUR][1000 genomes]
rs6787422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792461	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792488	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6800271	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73081205	0.83[EUR][1000 genomes]
rs7613282	0.87[EUR][1000 genomes]
rs7628631	0.80[EUR][1000 genomes]
rs7641010	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649234	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7651194	0.81[EUR][1000 genomes]
rs7651762	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs807810	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs807931	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8180040	0.86[EUR][1000 genomes]
rs878659	0.88[EUR][1000 genomes]
rs922957	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9683033	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9683177	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11925823	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11925823	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47423600-47446000	Weak transcription	Colonic Mucosa	Colon
2	chr3:47423800-47447400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:47423800-47448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:47423800-47449800	Weak transcription	A549	lung
5	chr3:47424000-47446000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:47427600-47448400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:47428200-47449000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:47430200-47449600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:47431000-47448600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:47434000-47447400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:47436000-47446200	Strong transcription	Fetal Intestine Small	intestine
13	chr3:47436000-47454600	Weak transcription	Hela-S3	cervix
14	chr3:47436200-47462000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:47436400-47443600	Strong transcription	Dnd41	blood
16	chr3:47436400-47446000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:47436400-47446000	Strong transcription	Fetal Stomach	stomach
18	chr3:47436600-47446000	Weak transcription	Stomach Mucosa	stomach
19	chr3:47436600-47447800	Weak transcription	Small Intestine	intestine
20	chr3:47436600-47454800	Weak transcription	Fetal Kidney	kidney
21	chr3:47436800-47446200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:47436800-47447800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:47437000-47443600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:47437000-47444200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:47437000-47446000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:47437000-47448200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:47437000-47450000	Weak transcription	HUVEC	blood vessel
28	chr3:47437200-47446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:47437200-47446000	Weak transcription	Gastric	stomach
30	chr3:47437400-47443600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:47437400-47444200	Strong transcription	Placenta	Placenta
32	chr3:47437400-47446000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:47437600-47446000	Weak transcription	Pancreas	Pancrea
34	chr3:47437600-47453400	Weak transcription	Psoas Muscle	Psoas
35	chr3:47437800-47462800	Weak transcription	Fetal Brain Male	brain
36	chr3:47438200-47444000	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:47438400-47446000	Weak transcription	Aorta	Aorta
38	chr3:47438400-47446000	Weak transcription	K562	blood
39	chr3:47438400-47446200	Weak transcription	Esophagus	oesophagus
40	chr3:47438600-47445600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:47438800-47446200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:47439000-47446200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:47439000-47448000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:47439000-47448800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:47439200-47449200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:47439200-47455000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:47439400-47445200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:47440400-47446000	Weak transcription	Fetal Lung	lung
49	chr3:47440800-47446000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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