Variant report

Variant	rs2079131
Chromosome Location	chr4:110550818-110550819
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10010159	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10017027	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10020263	0.95[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10032323	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1008326	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1029449	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1029450	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1029451	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1042891	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098036	0.80[CEU][hapmap]
rs11098039	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098040	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11724306	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931318	0.81[ASN][1000 genomes]
rs11937120	0.82[AMR][1000 genomes]
rs12498588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12504296	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12504784	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12511995	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646055	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12647060	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13103167	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13112432	0.85[ASN][1000 genomes]
rs13151303	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1476545	0.80[CEU][hapmap]
rs197231	0.82[CEU][hapmap]
rs2107050	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2107051	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285712	0.95[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28380238	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28850086	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28892996	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3181191	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3182325	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34925690	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35838666	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733611	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756256	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796911	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796912	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4698744	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698745	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698747	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4698748	0.95[CEU][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4698776	0.80[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4698777	0.95[EUR][1000 genomes]
rs4698780	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5030594	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5030606	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs59207576	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60916792	0.98[ASN][1000 genomes]
rs6533438	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6533444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533445	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815377	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6816926	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6825095	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6831930	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6833490	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834082	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6834701	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849691	0.91[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6851190	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6851356	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6856535	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726583	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726584	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726585	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs735642	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763370	0.90[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7672819	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767598	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7699736	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699969	0.81[ASN][1000 genomes]
rs9990765	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9993532	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996648	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996730	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2079131	CCDC109B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110533000-110573000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:110533400-110552800	Weak transcription	Primary B cells from cord blood	blood
3	chr4:110536000-110552800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:110536400-110552800	Weak transcription	Adipose Nuclei	Adipose
5	chr4:110536400-110552800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:110538400-110552000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:110544200-110552800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:110544200-110552800	Weak transcription	Ovary	ovary
9	chr4:110545200-110552800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:110545400-110552800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:110546000-110559600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:110546200-110551000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:110546200-110552000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:110546200-110552600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:110546200-110552600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:110546200-110552800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:110546200-110552800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:110546200-110552800	Weak transcription	Small Intestine	intestine
19	chr4:110546200-110566400	Weak transcription	Fetal Thymus	thymus
20	chr4:110546400-110552800	Weak transcription	Right Atrium	heart
21	chr4:110546600-110580600	Weak transcription	Thymus	Thymus
22	chr4:110548000-110554200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr4:110548400-110553600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:110548600-110553800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:110549200-110551200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr4:110549400-110551200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr4:110549600-110552000	Weak transcription	Fetal Intestine Small	intestine
28	chr4:110549600-110552600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:110549800-110552600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:110549800-110552600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:110550000-110551800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:110550200-110552000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr4:110550200-110552800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr4:110550600-110551000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:110550600-110551400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:110550600-110551600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:110550600-110569200	Weak transcription	GM12878-XiMat	blood
38	chr4:110550800-110551200	Enhancers	Placenta	Placenta
39	chr4:110550800-110551400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr4:110550800-110551400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr4:110550800-110551400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr4:110550800-110551600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:110550800-110551600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr4:110550800-110551600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:110550800-110552000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr4:110550800-110552000	Enhancers	A549	lung
47	chr4:110550800-110553400	Genic enhancers	Primary T cells from cord blood	blood

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