Variant report

Variant	rs4688688
Chromosome Location	chr3:50042690-50042691
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1061474	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10865959	0.88[CHB][hapmap]
rs11130233	0.84[JPT][hapmap]
rs1138536	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11709573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11712056	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11714324	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11721204	0.88[ASN][1000 genomes]
rs12107768	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12634780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13077403	0.91[ASN][1000 genomes]
rs13079006	0.88[ASN][1000 genomes]
rs13082703	0.95[ASN][1000 genomes]
rs1317140	0.89[CHB][hapmap]
rs17657664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17657688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1799843	0.89[CHB][hapmap]
rs1799845	0.89[CHB][hapmap]
rs2240328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2247510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2276864	0.86[CHB][hapmap]
rs2352969	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352975	0.90[CHB][hapmap]
rs2352984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2526747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2526749	0.85[ASN][1000 genomes]
rs2526750	0.82[ASN][1000 genomes]
rs2624815	0.88[ASN][1000 genomes]
rs2624817	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2624819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2624821	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2624822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2624826	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2624832	0.95[ASN][1000 genomes]
rs2624834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2681776	0.95[ASN][1000 genomes]
rs2681779	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2856237	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2856238	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2883059	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs34034116	0.88[ASN][1000 genomes]
rs34312088	0.95[ASN][1000 genomes]
rs34654589	0.81[ASN][1000 genomes]
rs35275715	0.88[ASN][1000 genomes]
rs3733134	0.88[ASN][1000 genomes]
rs3774734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3774759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3796386	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4688753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4688754	0.88[ASN][1000 genomes]
rs55692411	0.80[ASN][1000 genomes]
rs62262114	0.88[ASN][1000 genomes]
rs6446194	0.82[ASN][1000 genomes]
rs6446195	0.88[ASN][1000 genomes]
rs6446197	0.84[ASN][1000 genomes]
rs6762477	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6774354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6793528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6799579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7430334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7615206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7626952	0.85[ASN][1000 genomes]
rs7627864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7627910	0.85[ASN][1000 genomes]
rs7634441	0.88[ASN][1000 genomes]
rs7648174	0.95[ASN][1000 genomes]
rs868891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs952594	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9682295	0.88[ASN][1000 genomes]
rs9821675	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4688688	RBM6	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:50005200-50046400	Weak transcription	Psoas Muscle	Psoas
6	chr3:50005200-50050600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
8	chr3:50008600-50050400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:50010800-50087000	Weak transcription	NHLF	lung
10	chr3:50011000-50046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:50011000-50046400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:50011000-50048400	Weak transcription	A549	lung
13	chr3:50011000-50051000	Weak transcription	Pancreas	Pancrea
14	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
16	chr3:50012400-50049000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:50015400-50046400	Weak transcription	Fetal Kidney	kidney
19	chr3:50018800-50043600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:50022200-50046400	Weak transcription	Gastric	stomach
21	chr3:50028000-50056400	Weak transcription	Ovary	ovary
22	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
23	chr3:50029800-50050800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
25	chr3:50031000-50048000	Strong transcription	Fetal Thymus	thymus
26	chr3:50033800-50051000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
28	chr3:50035600-50047200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:50036400-50046800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
31	chr3:50036800-50048000	Strong transcription	Fetal Stomach	stomach
32	chr3:50036800-50054600	Strong transcription	Fetal Intestine Small	intestine
33	chr3:50037200-50042800	Strong transcription	Placenta	Placenta
34	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:50037600-50043600	Weak transcription	Spleen	Spleen
36	chr3:50037600-50044600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:50037600-50046200	Weak transcription	NHEK	skin
38	chr3:50037600-50046400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:50037600-50046600	Weak transcription	Lung	lung
40	chr3:50037600-50049200	Weak transcription	Brain Germinal Matrix	brain
41	chr3:50037600-50055400	Weak transcription	Hela-S3	cervix
42	chr3:50037600-50061800	Weak transcription	Small Intestine	intestine
43	chr3:50037800-50044800	Weak transcription	GM12878-XiMat	blood
44	chr3:50037800-50046200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:50038800-50056800	Weak transcription	HepG2	liver
48	chr3:50039000-50046200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:50039000-50046400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:50039400-50043600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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