Variant report

Variant	rs10169395
Chromosome Location	chr2:55628936-55628937
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55627632..55629326-chr2:55632488..55634437,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10172058	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10191937	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10194425	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap]
rs10496042	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]
rs11125573	0.84[CHB][hapmap];0.85[YRI][hapmap]
rs11678347	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11902837	0.80[ASN][1000 genomes]
rs12470528	0.83[AFR][1000 genomes]
rs12614357	0.82[ASN][1000 genomes]
rs12617887	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12621289	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12621495	0.87[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12623605	0.86[CHB][hapmap]
rs12713293	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713294	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713295	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12713296	0.86[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12991401	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13001912	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13010237	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13010255	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13013113	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13019339	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13022424	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13028925	0.92[ASN][1000 genomes]
rs13389156	0.85[CHB][hapmap]
rs1349884	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349885	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370360	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs1370361	0.81[YRI][hapmap]
rs1437394	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs1902060	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1992127	0.84[YRI][hapmap]
rs1992128	0.81[YRI][hapmap]
rs2198575	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576706	0.81[YRI][hapmap]
rs2589055	0.81[YRI][hapmap]
rs2589084	0.82[YRI][hapmap]
rs2589085	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2589087	0.84[YRI][hapmap]
rs2589105	0.81[AFR][1000 genomes]
rs2867174	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867175	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867176	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867177	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920971	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs3111404	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs3111413	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs3791642	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3791650	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs3791652	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3828235	0.86[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66882175	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6724338	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6727038	0.81[YRI][hapmap]
rs6746104	0.87[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6747649	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs6752182	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6754930	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6756777	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74181227	0.97[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7558687	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7561473	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7569535	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572492	0.81[EUR][1000 genomes]
rs7589390	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7600339	0.82[ASN][1000 genomes]
rs7606505	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9789365	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]

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	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
3	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
4	esv275364	chr2:55621732-55632233	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10169395	CCDC88A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
4	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
8	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
13	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
15	chr2:55600600-55631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:55600800-55629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:55600800-55629400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:55602000-55629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:55602200-55629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:55602400-55629600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:55603600-55629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:55603600-55630200	Weak transcription	NH-A	brain
25	chr2:55606200-55630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:55608600-55630400	Weak transcription	HSMM	muscle
27	chr2:55612600-55629600	Weak transcription	Dnd41	blood
28	chr2:55612600-55630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
30	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
31	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:55616600-55635400	Weak transcription	HMEC	breast
33	chr2:55616800-55630200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
35	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
36	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
37	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
39	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:55619000-55630200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:55619000-55632200	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:55619200-55629400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:55619600-55630400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:55619600-55632000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:55622600-55630400	Weak transcription	K562	blood
47	chr2:55623000-55635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
49	chr2:55623600-55629400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:55623600-55630200	Weak transcription	Brain Cingulate Gyrus	brain

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