Variant report

Variant	rs1045613
Chromosome Location	chr2:55516090-55516091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55512725..55515035-chr2:55515151..55518093,2	MCF-7	breast:
2	chr2:55513717..55517670-chr2:55518024..55521740,6	K562	blood:
3	chr2:55514301..55516151-chr2:55518959..55520928,3	MCF-7	breast:
4	chr2:55516061..55518491-chr2:55518529..55520349,2	K562	blood:

Variant related genes	Relation type
ENSG00000206964	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10496042	0.81[ASW][hapmap];0.85[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11678347	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12614357	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12617887	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12621289	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12621495	0.80[CEU][hapmap]
rs12623137	0.83[CHB][hapmap]
rs12713293	0.81[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs12713294	0.81[AMR][1000 genomes]
rs12713295	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs12713296	0.81[ASW][hapmap];0.80[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs13001912	0.81[AMR][1000 genomes]
rs13010237	0.82[AMR][1000 genomes]
rs13013113	0.85[CEU][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs13019339	0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13022424	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13028925	0.80[AMR][1000 genomes]
rs13389156	0.85[TSI][hapmap]
rs1349884	0.81[AMR][1000 genomes]
rs1349885	0.85[CEU][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs1370360	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1370361	1.00[CEU][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1437396	0.82[CHB][hapmap]
rs1902060	0.80[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs2198575	0.81[AMR][1000 genomes]
rs2867174	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs2867175	0.82[AMR][1000 genomes]
rs2867176	0.81[AMR][1000 genomes]
rs3791650	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs3791652	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3828235	0.80[CEU][hapmap];0.85[GIH][hapmap];0.80[TSI][hapmap]
rs66728407	0.86[ASN][1000 genomes]
rs66882175	0.81[AMR][1000 genomes]
rs6746104	0.80[CEU][hapmap]
rs6747649	0.80[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs6752182	0.82[AMR][1000 genomes]
rs6754930	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6756777	0.82[AMR][1000 genomes]
rs74181227	0.81[AMR][1000 genomes]
rs7558687	0.80[CEU][hapmap];0.81[AMR][1000 genomes]
rs7561473	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7572492	0.93[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7589390	0.81[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs7600339	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9789365	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][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

No data

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	chr2:55510000-55516200	Weak transcription	Fetal Lung	lung
8	chr2:55510000-55518800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:55510000-55521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:55510000-55521600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:55510000-55521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:55510000-55521800	Weak transcription	Fetal Brain Male	brain
13	chr2:55510000-55521800	Weak transcription	NHEK	skin
14	chr2:55510000-55522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:55510000-55522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55510000-55522200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:55510000-55522400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55510000-55522400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:55510000-55522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
21	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:55510200-55516200	Weak transcription	NHDF-Ad	bronchial
24	chr2:55510200-55516600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:55510200-55517400	Weak transcription	Fetal Brain Female	brain
26	chr2:55510200-55519200	Weak transcription	Ovary	ovary
27	chr2:55510200-55520600	Weak transcription	HSMMtube	muscle
28	chr2:55510200-55521800	Weak transcription	Fetal Kidney	kidney
29	chr2:55510200-55522200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:55510200-55522400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:55510200-55522400	Weak transcription	NHLF	lung
32	chr2:55510200-55522600	Weak transcription	Aorta	Aorta
33	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
34	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
35	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
36	chr2:55510400-55522400	Weak transcription	Left Ventricle	heart
37	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
38	chr2:55510600-55519400	Weak transcription	Primary B cells from cord blood	blood
39	chr2:55510600-55521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:55510600-55522400	Weak transcription	A549	lung
41	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
42	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:55510600-55537400	Weak transcription	Lung	lung
44	chr2:55510800-55518200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:55510800-55518600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:55510800-55521200	Weak transcription	Osteobl	bone
47	chr2:55510800-55521800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:55511000-55518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:55511000-55519600	Weak transcription	Primary T cells fromperipheralblood	blood

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