Variant report

Variant	rs3791650
Chromosome Location	chr2:55592318-55592319
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55584108..55586165-chr2:55591531..55593375,2	K562	blood:
2	chr2:55586524..55588974-chr2:55589647..55593883,3	K562	blood:
3	chr2:55592018..55593531-chr2:55595519..55597043,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10169395	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10172058	0.86[ASN][1000 genomes]
rs10191937	0.85[EUR][1000 genomes]
rs10194425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1045613	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10496042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125564	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125573	0.90[CHB][hapmap]
rs11678347	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11891739	0.81[CEU][hapmap]
rs12614357	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12617887	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621495	0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12623605	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs12713293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713294	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713296	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs12991401	0.82[EUR][1000 genomes]
rs13001912	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13010237	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13010255	0.86[EUR][1000 genomes]
rs13013113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13019339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022424	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13028925	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13389156	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs1349884	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1349885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1370360	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370361	0.86[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs1545555	0.89[YRI][hapmap]
rs1902060	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2198575	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2576715	0.86[YRI][hapmap]
rs2589102	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs2864830	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs2867174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867175	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867176	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867177	0.89[ASN][1000 genomes]
rs2917776	0.89[YRI][hapmap]
rs3099075	0.84[AFR][1000 genomes]
rs3099076	0.84[AFR][1000 genomes]
rs3099077	0.84[AFR][1000 genomes]
rs3099079	0.81[AFR][1000 genomes]
rs3099082	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs3099084	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs3111410	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs3111411	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs3111412	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs35963448	0.81[AFR][1000 genomes]
rs3791642	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791653	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs3828235	0.95[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs57410428	0.81[AFR][1000 genomes]
rs66882175	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724338	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6725124	0.89[YRI][hapmap]
rs6746104	0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs6747649	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs6752182	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754930	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756777	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74181227	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558687	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561473	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7569535	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7572492	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7582580	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs7586529	0.81[AFR][1000 genomes]
rs7589390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7600339	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7603216	0.90[YRI][hapmap]
rs7606505	0.85[EUR][1000 genomes]
rs9789365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[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	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3791650	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:55537800-55609400	Weak transcription	Lung	lung
4	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
5	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:55558400-55595000	Weak transcription	Fetal Heart	heart
7	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney
8	chr2:55572000-55610200	Weak transcription	Liver	Liver
9	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:55579200-55602200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
12	chr2:55579400-55596200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:55579400-55614400	Weak transcription	Fetal Brain Female	brain
14	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
16	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:55582200-55603600	Weak transcription	Ovary	ovary
19	chr2:55582800-55615000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:55583200-55605000	Weak transcription	HepG2	liver
21	chr2:55583400-55597400	Weak transcription	Fetal Stomach	stomach
22	chr2:55583400-55602000	Weak transcription	Left Ventricle	heart
23	chr2:55583400-55602400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:55583600-55606800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr2:55583600-55607200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:55584200-55597000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:55584200-55612000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:55584400-55598800	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:55584600-55598000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:55584600-55599600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:55587400-55602000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:55588800-55593000	Enhancers	Brain Hippocampus Middle	brain
33	chr2:55589000-55593000	Enhancers	Brain Anterior Caudate	brain
34	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
35	chr2:55589600-55595000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:55589600-55599600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:55589600-55628800	Weak transcription	Fetal Thymus	thymus
38	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:55590200-55593000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr2:55590200-55594600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr2:55590200-55599800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:55590400-55593000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:55590400-55622400	Weak transcription	GM12878-XiMat	blood
44	chr2:55590600-55593000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:55590600-55593200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:55590800-55592800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:55590800-55592800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:55590800-55592800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr2:55590800-55592800	Enhancers	Osteobl	bone
50	chr2:55590800-55593400	Enhancers	HUVEC	blood vessel

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