Variant report

Variant	rs10194425
Chromosome Location	chr2:55587004-55587005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55567779..55569483-chr2:55585601..55588441,2	MCF-7	breast:
2	chr2:55586524..55588974-chr2:55589647..55593883,3	K562	blood:
3	chr2:55579484..55583558-chr2:55584922..55587594,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10169395	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs10189439	0.83[YRI][hapmap]
rs10496042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs11125573	0.89[CHB][hapmap]
rs12621289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12621495	0.85[CHB][hapmap];0.88[YRI][hapmap]
rs12623605	0.90[CHB][hapmap]
rs12713293	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs12713295	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs12713296	0.84[CHB][hapmap];0.82[YRI][hapmap]
rs13013113	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs13019339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs13389156	0.90[CHB][hapmap]
rs1349885	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1370360	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1370361	0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs1902060	0.90[CHB][hapmap];0.87[YRI][hapmap]
rs1992127	0.88[YRI][hapmap]
rs1992128	0.85[YRI][hapmap]
rs2198575	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2576705	0.83[YRI][hapmap]
rs2576706	0.85[YRI][hapmap]
rs2589055	0.85[YRI][hapmap]
rs2589066	0.82[YRI][hapmap]
rs2867174	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs3111413	0.82[YRI][hapmap]
rs3791633	0.84[YRI][hapmap]
rs3791634	0.87[YRI][hapmap]
rs3791642	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3791650	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3791652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs3828235	0.90[CHB][hapmap];0.83[YRI][hapmap]
rs6724338	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6727038	0.85[YRI][hapmap]
rs6746104	0.90[CHB][hapmap];0.85[YRI][hapmap]
rs6747649	0.90[CHB][hapmap];0.87[YRI][hapmap]
rs7558687	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7569535	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs7589390	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs9789365	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][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	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
5	esv3341640	chr2:55586989-55587431	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10194425	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 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	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
7	chr2:55537800-55609400	Weak transcription	Lung	lung
8	chr2:55542400-55589800	Weak transcription	Fetal Intestine Large	intestine
9	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
10	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:55554800-55591600	Weak transcription	HSMMtube	muscle
12	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:55558400-55595000	Weak transcription	Fetal Heart	heart
14	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney
15	chr2:55572000-55610200	Weak transcription	Liver	Liver
16	chr2:55573800-55590800	Weak transcription	HUVEC	blood vessel
17	chr2:55574600-55591800	Weak transcription	HMEC	breast
18	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:55576800-55590800	Weak transcription	NH-A	brain
20	chr2:55578400-55590600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:55579200-55591200	Weak transcription	NHEK	skin
22	chr2:55579200-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:55579200-55602200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
25	chr2:55579400-55588600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:55579400-55588600	Weak transcription	GM12878-XiMat	blood
27	chr2:55579400-55591600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:55579400-55592000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:55579400-55596200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:55579400-55614400	Weak transcription	Fetal Brain Female	brain
31	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
33	chr2:55579600-55590800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:55580600-55591400	Weak transcription	A549	lung
36	chr2:55581400-55592000	Weak transcription	K562	blood
37	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:55582200-55603600	Weak transcription	Ovary	ovary
39	chr2:55582600-55589000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:55582800-55615000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:55583000-55589000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:55583000-55590600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:55583000-55591200	Weak transcription	NHLF	lung
44	chr2:55583000-55591600	Weak transcription	Adipose Nuclei	Adipose
45	chr2:55583200-55589000	Weak transcription	Hela-S3	cervix
46	chr2:55583200-55605000	Weak transcription	HepG2	liver
47	chr2:55583400-55588600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:55583400-55588800	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:55583400-55590000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:55583400-55590200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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