Variant report

Variant	rs10496042
Chromosome Location	chr2:55599810-55599811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55597784..55600046-chr2:55608046..55611475,3	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10169061	0.81[AMR][1000 genomes]
rs10169395	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10172058	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10189439	0.94[ASW][hapmap];0.98[LWK][hapmap];0.84[AFR][1000 genomes]
rs10191937	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10194425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs1045613	0.81[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125564	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125573	0.89[CHB][hapmap];0.91[YRI][hapmap]
rs11678347	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11891739	0.80[CEU][hapmap]
rs11902837	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12470528	0.90[AFR][1000 genomes]
rs12614357	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12617887	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12621289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621495	0.95[CEU][hapmap];0.82[CHB][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12623605	0.81[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs12713293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713294	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713296	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12713298	0.80[EUR][1000 genomes]
rs12991401	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13001912	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13010237	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13010255	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13013113	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13019339	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022424	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13028925	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13389156	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs13423775	0.80[EUR][1000 genomes]
rs1349884	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1349885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1370360	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370361	0.85[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1437394	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs1902060	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1992127	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs1992128	0.82[AFR][1000 genomes]
rs2198575	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249856	0.91[LWK][hapmap]
rs2576705	0.94[ASW][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.80[AFR][1000 genomes]
rs2576706	0.83[AFR][1000 genomes]
rs2589055	0.82[AFR][1000 genomes]
rs2589056	0.84[AFR][1000 genomes]
rs2589066	0.84[AFR][1000 genomes]
rs2589077	0.80[MEX][hapmap]
rs2589084	0.84[YRI][hapmap]
rs2589085	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2589087	0.84[YRI][hapmap]
rs2589105	0.87[AFR][1000 genomes]
rs2589106	0.86[AFR][1000 genomes]
rs2589113	0.86[LWK][hapmap]
rs2867174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867175	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867176	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867177	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28672687	0.80[EUR][1000 genomes]
rs2920971	0.94[ASW][hapmap];0.98[LWK][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes]
rs3111404	0.88[YRI][hapmap];0.90[AFR][1000 genomes]
rs3111413	0.84[YRI][hapmap];0.90[AFR][1000 genomes]
rs3791633	0.84[AFR][1000 genomes]
rs3791634	0.84[AFR][1000 genomes]
rs3791642	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791650	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]
rs3791652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828235	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56978967	0.80[EUR][1000 genomes]
rs6545487	0.81[AFR][1000 genomes]
rs6545488	0.84[AFR][1000 genomes]
rs66882175	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724338	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6727038	0.83[AFR][1000 genomes]
rs6746104	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6747649	0.94[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6752182	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754930	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756777	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74181227	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7558687	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561473	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7569535	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7572492	0.88[ASW][hapmap];0.85[CEU][hapmap];0.92[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7589390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7600339	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606505	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9789365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10496042	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL
rs10496042	EML6	cis	parietal	SCAN

Chromatin state (count:80 , 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	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney
7	chr2:55572000-55610200	Weak transcription	Liver	Liver
8	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:55579200-55602200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
11	chr2:55579400-55614400	Weak transcription	Fetal Brain Female	brain
12	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
14	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55582200-55603600	Weak transcription	Ovary	ovary
17	chr2:55582800-55615000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:55583200-55605000	Weak transcription	HepG2	liver
19	chr2:55583400-55602000	Weak transcription	Left Ventricle	heart
20	chr2:55583400-55602400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:55583600-55606800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:55583600-55607200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:55584200-55612000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:55587400-55602000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
26	chr2:55589600-55628800	Weak transcription	Fetal Thymus	thymus
27	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:55590400-55622400	Weak transcription	GM12878-XiMat	blood
29	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:55592200-55600200	Weak transcription	Adipose Nuclei	Adipose
32	chr2:55592200-55617600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:55592800-55609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:55592800-55609600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:55592800-55615600	Weak transcription	NHEK	skin
37	chr2:55592800-55617800	Weak transcription	A549	lung
38	chr2:55592800-55626600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
40	chr2:55593000-55622400	Weak transcription	Brain Angular Gyrus	brain
41	chr2:55593000-55622400	Weak transcription	Brain Anterior Caudate	brain
42	chr2:55593200-55611000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:55593400-55616400	Weak transcription	HUVEC	blood vessel
45	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
46	chr2:55594400-55603600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:55595400-55605000	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:55596600-55603600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:55596600-55608400	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:55597400-55601800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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