Variant report

Variant	rs2589113
Chromosome Location	chr2:55516323-55516324
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55516323..55518543-chr2:55519705..55522425,2	MCF-7	breast:
2	chr2:55495242..55497992-chr2:55516142..55518443,2	K562	blood:
3	chr2:55512725..55515035-chr2:55515151..55518093,2	MCF-7	breast:
4	chr2:55513717..55517670-chr2:55518024..55521740,6	K562	blood:
5	chr2:55516061..55518491-chr2:55518529..55520349,2	K562	blood:

Variant related genes	Relation type
ENSG00000206964	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10183953	0.82[JPT][hapmap]
rs10189439	0.88[LWK][hapmap]
rs10209598	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10439479	0.82[JPT][hapmap]
rs10496041	0.94[ASN][1000 genomes]
rs10496042	0.86[LWK][hapmap]
rs11125562	1.00[ASN][1000 genomes]
rs11125563	0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs11694920	0.82[JPT][hapmap]
rs11884753	0.87[AFR][1000 genomes]
rs11892007	1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11904107	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12104902	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12105322	1.00[ASN][1000 genomes]
rs12105731	1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12617316	1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713293	0.86[LWK][hapmap]
rs13013113	0.82[LWK][hapmap]
rs13016664	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019339	0.86[LWK][hapmap]
rs13031346	0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13407931	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1437387	1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1437388	1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1437389	0.82[JPT][hapmap]
rs1437392	0.82[JPT][hapmap]
rs1545120	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545121	0.91[GIH][hapmap];0.82[YRI][hapmap]
rs1561231	0.82[JPT][hapmap]
rs17046834	1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2043714	0.82[JPT][hapmap]
rs2118283	0.82[JPT][hapmap]
rs2249856	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289168	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2576691	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576692	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576693	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576694	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576697	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2576698	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2576699	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs2576702	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2576705	0.88[LWK][hapmap]
rs2589058	0.90[AFR][1000 genomes]
rs2589060	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589061	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589067	0.85[ASN][1000 genomes]
rs2589081	0.82[JPT][hapmap]
rs2589082	0.82[JPT][hapmap]
rs2589110	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589111	1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589112	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589114	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2589115	0.85[ASN][1000 genomes]
rs2589116	1.00[ASN][1000 genomes]
rs2589117	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917775	0.90[AFR][1000 genomes]
rs2917781	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920959	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920971	0.88[LWK][hapmap]
rs2920972	1.00[ASN][1000 genomes]
rs2920973	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs2966465	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4233959	0.82[JPT][hapmap]
rs4591380	0.82[JPT][hapmap]
rs57105158	1.00[ASN][1000 genomes]
rs59554860	0.94[ASN][1000 genomes]
rs6545476	0.82[JPT][hapmap]
rs6545479	0.82[JPT][hapmap]
rs6545482	1.00[JPT][hapmap]
rs6545484	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6705991	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6713058	0.82[JPT][hapmap]
rs6715694	0.82[JPT][hapmap]
rs6716066	0.82[JPT][hapmap]
rs6718747	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719579	0.82[JPT][hapmap]
rs6721211	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6723870	0.82[JPT][hapmap]
rs6726732	1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6733567	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6738970	0.84[ASW][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs6739348	0.85[AFR][1000 genomes]
rs6740631	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746287	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6747682	0.82[JPT][hapmap]
rs6750501	0.82[JPT][hapmap]
rs73939905	1.00[ASN][1000 genomes]
rs7589390	0.81[LWK][hapmap]
rs9784090	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	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
6	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

Variant related diseases (count:1)

Disease	PMID	Source
Height	21998595	GWAS catalog

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55501000-55517000	Weak transcription	Hela-S3	cervix
2	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:55509600-55522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:55509800-55518600	Weak transcription	HMEC	breast
6	chr2:55509800-55521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:55510000-55518800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:55510000-55521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:55510000-55521600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:55510000-55521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:55510000-55521800	Weak transcription	Fetal Brain Male	brain
12	chr2:55510000-55521800	Weak transcription	NHEK	skin
13	chr2:55510000-55522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:55510000-55522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:55510000-55522200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:55510000-55522400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:55510000-55522400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:55510000-55522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
20	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:55510200-55516600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:55510200-55517400	Weak transcription	Fetal Brain Female	brain
24	chr2:55510200-55519200	Weak transcription	Ovary	ovary
25	chr2:55510200-55520600	Weak transcription	HSMMtube	muscle
26	chr2:55510200-55521800	Weak transcription	Fetal Kidney	kidney
27	chr2:55510200-55522200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:55510200-55522400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:55510200-55522400	Weak transcription	NHLF	lung
30	chr2:55510200-55522600	Weak transcription	Aorta	Aorta
31	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
32	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
33	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
34	chr2:55510400-55522400	Weak transcription	Left Ventricle	heart
35	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
36	chr2:55510600-55519400	Weak transcription	Primary B cells from cord blood	blood
37	chr2:55510600-55521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:55510600-55522400	Weak transcription	A549	lung
39	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
40	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:55510600-55537400	Weak transcription	Lung	lung
42	chr2:55510800-55518200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:55510800-55518600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:55510800-55521200	Weak transcription	Osteobl	bone
45	chr2:55510800-55521800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:55511000-55518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:55511000-55519600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr2:55511000-55521600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:55511000-55521800	Weak transcription	H1 Cell Line	embryonic stem cell

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