Variant report

Variant	rs3099081
Chromosome Location	chr2:55590429-55590430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55586524..55588974-chr2:55589647..55593883,3	K562	blood:
2	chr1:212458271..212459805-chr2:55589892..55591748,2	K562	blood:
3	chr2:55570093..55571972-chr2:55587892..55590606,2	K562	blood:
4	chr2:55589556..55591958-chr2:55592375..55594974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10182704	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10184756	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10195081	0.83[ASN][1000 genomes]
rs10198652	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs10454144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125565	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125566	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11125568	0.87[CHB][hapmap]
rs11125569	0.81[CHB][hapmap]
rs12612806	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12617891	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12618795	0.82[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes]
rs12623954	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13416912	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1454420	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1454423	0.90[EUR][1000 genomes]
rs1454424	0.83[EUR][1000 genomes]
rs1545554	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1902056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1902057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1902058	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1902061	0.82[CEU][hapmap]
rs2043713	0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2045132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2045133	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2123983	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2219130	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576688	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2576703	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589057	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589068	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589069	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589070	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589078	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589079	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589104	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864831	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864832	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867173	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2867178	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2867179	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2867194	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2902857	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2903509	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903514	0.90[EUR][1000 genomes]
rs2917777	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920963	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2920970	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966466	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099080	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3111408	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3111409	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3748943	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs3762511	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3974263	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233960	1.00[CEU][hapmap];0.94[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];0.96[ASN][1000 genomes]
rs4233961	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4481025	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4484068	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4535081	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4672030	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4672032	0.82[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes]
rs4672033	0.90[EUR][1000 genomes]
rs4672035	0.86[CHB][hapmap]
rs4672036	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4672037	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4672038	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4672041	0.90[EUR][1000 genomes]
rs59634508	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61157332	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545476	1.00[YRI][hapmap]
rs6545489	0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs6545490	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6545491	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6709204	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6710192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6718031	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6718909	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721593	0.82[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6724840	0.82[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs6725968	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6732759	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6744426	0.87[EUR][1000 genomes]
rs6748979	0.90[EUR][1000 genomes]
rs72924907	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355381	0.89[ASN][1000 genomes]
rs7557555	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7557956	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7559987	0.87[CHB][hapmap]
rs7574743	0.94[ASN][1000 genomes]
rs7586440	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes]
rs7589279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7595396	0.82[AMR][1000 genomes]
rs7601588	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7603105	0.93[ASN][1000 genomes]
rs7606361	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9751964	0.91[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

No data

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	chr2:55537800-55609400	Weak transcription	Lung	lung
7	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
8	chr2:55547400-55590600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:55554800-55591600	Weak transcription	HSMMtube	muscle
10	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:55558400-55595000	Weak transcription	Fetal Heart	heart
12	chr2:55564200-55605200	Weak transcription	Fetal Kidney	kidney
13	chr2:55572000-55610200	Weak transcription	Liver	Liver
14	chr2:55573800-55590800	Weak transcription	HUVEC	blood vessel
15	chr2:55574600-55591800	Weak transcription	HMEC	breast
16	chr2:55576000-55612200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:55576800-55590800	Weak transcription	NH-A	brain
18	chr2:55578400-55590600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:55579200-55591200	Weak transcription	NHEK	skin
20	chr2:55579200-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:55579200-55602200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
23	chr2:55579400-55591600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:55579400-55592000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:55579400-55596200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:55579400-55614400	Weak transcription	Fetal Brain Female	brain
27	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
29	chr2:55579600-55590800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:55580600-55591400	Weak transcription	A549	lung
32	chr2:55581400-55592000	Weak transcription	K562	blood
33	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:55582200-55603600	Weak transcription	Ovary	ovary
35	chr2:55582800-55615000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:55583000-55590600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:55583000-55591200	Weak transcription	NHLF	lung
38	chr2:55583000-55591600	Weak transcription	Adipose Nuclei	Adipose
39	chr2:55583200-55605000	Weak transcription	HepG2	liver
40	chr2:55583400-55592000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:55583400-55597400	Weak transcription	Fetal Stomach	stomach
42	chr2:55583400-55602000	Weak transcription	Left Ventricle	heart
43	chr2:55583400-55602400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:55583600-55591800	Weak transcription	Fetal Lung	lung
45	chr2:55583600-55606800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:55583600-55607200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:55584200-55597000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:55584200-55612000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:55584400-55598800	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:55584600-55598000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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