Variant report

Variant	rs2903509
Chromosome Location	chr2:55629724-55629725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:55629287-55629763	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55624788..55628704-chr2:55629085..55632054,3	K562	blood:
2	chr2:55629328..55632200-chr2:55634808..55637417,2	K562	blood:
3	chr2:55629189..55632200-chr2:55632234..55637417,4	K562	blood:
4	chr2:55627338..55628874-chr2:55629453..55631312,2	MCF-7	breast:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10182704	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10184756	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];0.99[ASN][1000 genomes]
rs10198652	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10454144	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11125565	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11125566	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125568	0.84[CHB][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11125569	0.89[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11125572	0.96[YRI][hapmap]
rs12612806	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12618795	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12623954	0.93[EUR][1000 genomes]
rs13008631	0.88[AFR][1000 genomes]
rs13416912	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1454415	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1454419	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1454420	0.93[EUR][1000 genomes]
rs1454423	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1454424	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1545554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17735450	1.00[CEU][hapmap]
rs1902056	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902057	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1902058	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2043713	0.85[JPT][hapmap]
rs2045132	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2045133	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2045134	0.96[AFR][1000 genomes]
rs2045135	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2045136	0.91[AFR][1000 genomes]
rs2123983	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2219130	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576688	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2576703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2589057	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2589068	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2589069	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2589070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2589078	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2589079	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2589104	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2864831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2864832	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2867173	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2867178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2867179	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2867194	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2902857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903507	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2903514	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2917777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2920963	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2920970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2966466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099081	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3099083	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3111408	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3111409	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3748943	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3762511	0.93[EUR][1000 genomes]
rs3974263	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233961	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4277563	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4481025	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4484068	0.90[JPT][hapmap]
rs4535081	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4672030	0.82[ASN][1000 genomes]
rs4672032	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4672033	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4672034	0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4672035	0.83[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4672036	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4672037	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672038	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672040	0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4672041	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672043	0.80[AFR][1000 genomes]
rs56201519	0.93[AFR][1000 genomes]
rs58708869	0.93[AFR][1000 genomes]
rs59634508	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61157332	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545489	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545490	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545491	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545492	0.87[YRI][hapmap];0.91[AFR][1000 genomes]
rs6705104	0.95[AFR][1000 genomes]
rs6709204	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6718031	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6718909	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6720698	0.93[YRI][hapmap];0.95[AFR][1000 genomes]
rs6721593	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6724840	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6725968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732633	0.80[EUR][1000 genomes]
rs6732759	0.93[EUR][1000 genomes]
rs6733814	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6744426	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6748979	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72924907	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7355381	0.88[ASN][1000 genomes]
rs7424286	0.85[AFR][1000 genomes]
rs7557555	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7557956	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7559987	0.84[CHB][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7574743	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7579037	0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7586440	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7589279	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7601588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7602189	0.94[AFR][1000 genomes]
rs7603105	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7606361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9751964	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[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

No data

Chromatin state (count:81 , 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	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:55603600-55630200	Weak transcription	NH-A	brain
19	chr2:55606200-55630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:55608600-55630400	Weak transcription	HSMM	muscle
21	chr2:55612600-55630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
23	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
24	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:55616600-55635400	Weak transcription	HMEC	breast
26	chr2:55616800-55630200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
28	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
29	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
30	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
32	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:55619000-55630200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:55619000-55632200	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:55619600-55630400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:55619600-55632000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:55622600-55630400	Weak transcription	K562	blood
39	chr2:55623000-55635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
41	chr2:55623600-55630200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:55623600-55630200	Weak transcription	Brain Substantia Nigra	brain
43	chr2:55623600-55632200	Weak transcription	GM12878-XiMat	blood
44	chr2:55624200-55635600	Weak transcription	NHEK	skin
45	chr2:55624400-55645600	Weak transcription	Ovary	ovary
46	chr2:55624600-55632600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:55627000-55629800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr2:55627000-55631400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:55627400-55630200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr2:55627600-55630200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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