Variant report

Variant	rs7589279
Chromosome Location	chr2:55619320-55619321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55618745..55621738-chr2:55622062..55625126,3	K562	blood:
2	chr2:55617017..55619738-chr2:55645047..55647887,2	K562	blood:
3	chr2:55618238..55620708-chr2:55645047..55647010,2	K562	blood:
4	chr2:55617949..55620712-chr2:55634436..55637353,2	K562	blood:
5	chr2:55418148..55421092-chr2:55618955..55620570,2	K562	blood:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10169185	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10182704	0.97[ASN][1000 genomes]
rs10184756	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10195081	0.83[ASN][1000 genomes]
rs10198652	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs10454144	0.98[ASN][1000 genomes]
rs11125565	0.98[ASN][1000 genomes]
rs11125566	0.97[ASN][1000 genomes]
rs11125568	0.89[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125569	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125572	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11695152	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12612806	0.98[ASN][1000 genomes]
rs12617891	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12618795	0.88[CHB][hapmap]
rs13008631	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13416912	0.99[ASN][1000 genomes]
rs1454415	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1454419	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1545554	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1902056	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs1902057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1902058	0.97[ASN][1000 genomes]
rs1902061	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1902062	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2043713	0.85[JPT][hapmap]
rs2045132	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2045133	0.97[ASN][1000 genomes]
rs2045134	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2045135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045136	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2219130	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2576688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2576703	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2589057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2589068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2589069	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2589070	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2589078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2589079	0.90[ASN][1000 genomes]
rs2589104	0.91[ASN][1000 genomes]
rs2864831	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2864832	0.95[ASN][1000 genomes]
rs2867173	0.98[ASN][1000 genomes]
rs2867178	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2867179	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2902857	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2903507	0.97[ASN][1000 genomes]
rs2903509	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]
rs2917777	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2920963	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2920970	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2966466	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3099080	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3099081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3099083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3111408	0.86[ASN][1000 genomes]
rs3111409	0.86[ASN][1000 genomes]
rs3974263	0.97[ASN][1000 genomes]
rs4233960	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4233961	0.88[CHB][hapmap]
rs4277563	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4484068	0.90[JPT][hapmap];0.80[YRI][hapmap];0.80[ASN][1000 genomes]
rs4535081	0.89[ASN][1000 genomes]
rs4672030	0.88[ASN][1000 genomes]
rs4672032	0.88[CHB][hapmap]
rs4672034	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672035	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672040	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672043	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672044	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672045	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56201519	0.92[AFR][1000 genomes]
rs58708869	0.92[AFR][1000 genomes]
rs59634508	0.92[ASN][1000 genomes]
rs61157332	0.92[ASN][1000 genomes]
rs6545489	0.83[CHB][hapmap]
rs6545490	0.82[CHB][hapmap]
rs6545492	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6705104	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6709204	0.81[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6710192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6718031	0.97[ASN][1000 genomes]
rs6718909	0.95[ASN][1000 genomes]
rs6720698	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6724840	0.88[CHB][hapmap]
rs6725968	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6733814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72924907	0.93[ASN][1000 genomes]
rs7355381	0.91[ASN][1000 genomes]
rs7424286	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7557555	0.98[ASN][1000 genomes]
rs7557956	1.00[ASN][1000 genomes]
rs7559987	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7574743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7579037	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7583757	0.81[ASN][1000 genomes]
rs7586440	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs7601588	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7602189	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7603105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606361	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9751964	0.97[AFR][1000 genomes];0.96[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	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	nsv524437	chr2:55615366-55619923	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 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	chr2:55579400-55622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
6	chr2:55579600-55632200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:55582000-55632400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
9	chr2:55589600-55628800	Weak transcription	Fetal Thymus	thymus
10	chr2:55589600-55632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:55590400-55622400	Weak transcription	GM12878-XiMat	blood
12	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:55592000-55635400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:55592200-55631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:55592800-55626600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
17	chr2:55593000-55622400	Weak transcription	Brain Angular Gyrus	brain
18	chr2:55593000-55622400	Weak transcription	Brain Anterior Caudate	brain
19	chr2:55593200-55632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:55593800-55631800	Weak transcription	Brain Germinal Matrix	brain
21	chr2:55599200-55626800	Weak transcription	Osteobl	bone
22	chr2:55600600-55631600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:55600800-55629400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:55600800-55629400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:55601800-55631000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:55602000-55629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:55602200-55629600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:55602400-55629600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:55603600-55629400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:55603600-55630200	Weak transcription	NH-A	brain
32	chr2:55606200-55630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:55608600-55630400	Weak transcription	HSMM	muscle
34	chr2:55612600-55629600	Weak transcription	Dnd41	blood
35	chr2:55612600-55630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:55612800-55632000	Weak transcription	Fetal Stomach	stomach
37	chr2:55614200-55632000	Weak transcription	Thymus	Thymus
38	chr2:55616600-55635400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:55616600-55635400	Weak transcription	HMEC	breast
40	chr2:55616800-55622400	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:55616800-55630200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:55616800-55632200	Weak transcription	Hela-S3	cervix
43	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
44	chr2:55617400-55620000	Enhancers	K562	blood
45	chr2:55617600-55620000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:55617800-55619400	ZNF genes & repeats	A549	lung
47	chr2:55618200-55635200	Weak transcription	Psoas Muscle	Psoas
48	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
50	chr2:55618400-55619400	Weak transcription	Brain Cingulate Gyrus	brain

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