Variant report

Variant	rs6732746
Chromosome Location	chr2:64089748-64089749
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64078188..64080568-chr2:64088415..64090856,2	MCF-7	breast:
2	chr2:64066782..64070718-chr2:64080924..64091365,11	MCF-7	breast:
3	chr2:64067087..64069553-chr2:64087095..64089852,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10183479	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865344	0.82[AFR][1000 genomes]
rs11558741	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674020	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676710	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11683408	0.92[ASN][1000 genomes]
rs11686956	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11691987	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11693906	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11694253	0.83[ASN][1000 genomes]
rs11695421	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713498	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12996866	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018690	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13431781	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440002	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17562177	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17562423	0.90[ASN][1000 genomes]
rs17619753	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs193031	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2302808	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439183	0.88[ASN][1000 genomes]
rs2969395	0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs329478	0.88[ASN][1000 genomes]
rs329488	0.80[ASN][1000 genomes]
rs34122334	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34765999	0.88[ASN][1000 genomes]
rs34777730	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs35002211	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35336851	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35474183	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35480874	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35697586	0.88[ASN][1000 genomes]
rs35960986	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36033991	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36123537	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233930	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4538187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671071	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56904032	0.92[ASN][1000 genomes]
rs6546029	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546031	0.85[AFR][1000 genomes]
rs6546032	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546033	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66980330	1.00[ASN][1000 genomes]
rs6710763	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6715992	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67308158	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731508	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67615384	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67765474	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68117986	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72808243	0.96[ASN][1000 genomes]
rs72893103	0.92[ASN][1000 genomes]
rs7590399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597935	0.83[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS 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	30 gene(s)	inside rSNPs	diseases
2	esv3459595	chr2:64088179-64090097	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3459597	chr2:64088186-64090115	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3513333	chr2:64088206-64090089	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3513329	chr2:64088210-64090035	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3513331	chr2:64088230-64090039	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3513332	chr2:64088256-64090040	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3513334	chr2:64088260-64090035	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv3459598	chr2:64088315-64089993	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv3513335	chr2:64088315-64089993	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv16609	chr2:64088361-64089955	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6732746	UGP2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64070200-64103000	Weak transcription	Gastric	stomach
2	chr2:64077000-64100200	Weak transcription	Ovary	ovary
3	chr2:64078000-64108000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:64081800-64089800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:64081800-64100600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:64082200-64091400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr2:64082200-64092400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:64082200-64100200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:64082200-64110000	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:64083200-64090200	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:64083200-64091600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:64083200-64092000	Strong transcription	Fetal Lung	lung
15	chr2:64083200-64097800	Weak transcription	Right Atrium	heart
16	chr2:64083200-64110200	Weak transcription	Small Intestine	intestine
17	chr2:64083200-64110600	Weak transcription	Pancreas	Pancrea
18	chr2:64083400-64091600	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr2:64083600-64092000	Strong transcription	Placenta	Placenta
20	chr2:64083600-64095400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr2:64084000-64092000	Strong transcription	Adipose Nuclei	Adipose
22	chr2:64084000-64095600	Genic enhancers	Dnd41	blood
23	chr2:64084200-64094000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:64084600-64100000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:64084800-64092800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:64085000-64089800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:64085000-64090400	Strong transcription	Thymus	Thymus
28	chr2:64085000-64092600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:64085400-64092400	Strong transcription	Fetal Thymus	thymus
30	chr2:64085400-64093000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:64085400-64095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:64085400-64095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:64085400-64096600	Weak transcription	Brain Angular Gyrus	brain
34	chr2:64085400-64096600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:64085400-64098000	Weak transcription	Lung	lung
36	chr2:64085400-64098000	Weak transcription	Psoas Muscle	Psoas
37	chr2:64085400-64098400	Weak transcription	Aorta	Aorta
38	chr2:64085400-64100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:64085400-64100600	Weak transcription	Spleen	Spleen
40	chr2:64085600-64091200	Weak transcription	Brain Germinal Matrix	brain
41	chr2:64085600-64091800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:64085600-64092000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:64085600-64092600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:64085600-64102400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:64086400-64092200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:64086400-64092400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:64086400-64092400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:64086400-64092600	Strong transcription	HSMM	muscle
49	chr2:64086600-64096600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:64086600-64110000	Weak transcription	Esophagus	oesophagus

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