Variant report

Variant	rs6715992
Chromosome Location	chr2:64085344-64085345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64066782..64070718-chr2:64080924..64091365,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10183479	0.91[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865344	0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs11558741	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674020	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11676710	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11683408	0.92[ASN][1000 genomes]
rs11686956	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11691987	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11693906	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11694253	0.83[ASN][1000 genomes]
rs11695421	0.81[AFR][1000 genomes];0.86[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]
rs12991311	0.84[YRI][hapmap]
rs12996866	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006124	0.84[YRI][hapmap]
rs13018690	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13431781	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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];0.98[ASN][1000 genomes]
rs17562177	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17562423	0.90[ASN][1000 genomes]
rs17619753	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.86[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];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439183	0.88[ASN][1000 genomes]
rs2969395	0.92[CHB][hapmap];1.00[CHD][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];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34765999	0.88[ASN][1000 genomes]
rs34777730	0.91[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs35002211	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35336851	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35474183	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35480874	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35697586	0.88[ASN][1000 genomes]
rs35960986	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36033991	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36123537	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233930	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4538187	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];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671071	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs56904032	0.92[ASN][1000 genomes]
rs6546029	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546031	0.89[AFR][1000 genomes]
rs6546032	0.91[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546033	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66980330	1.00[ASN][1000 genomes]
rs6710230	0.84[YRI][hapmap]
rs6710763	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6726257	0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs67308158	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731508	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732746	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]
rs6755646	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67615384	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67765474	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68117986	0.92[ASN][1000 genomes]
rs72808243	0.96[ASN][1000 genomes]
rs72893103	0.92[ASN][1000 genomes]
rs7590399	0.91[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];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597935	0.83[MKK][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6715992	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	chr2:64077000-64089000	Weak transcription	Fetal Brain Male	brain
3	chr2:64077000-64100200	Weak transcription	Ovary	ovary
4	chr2:64078000-64108000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:64081800-64089800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:64081800-64100600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:64082200-64085400	Genic enhancers	Liver	Liver
8	chr2:64082200-64089600	Weak transcription	Stomach Mucosa	stomach
9	chr2:64082200-64091400	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr2:64082200-64092400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:64082200-64100200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:64082200-64110000	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:64082600-64085400	Strong transcription	HUVEC	blood vessel
14	chr2:64082600-64086800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:64082600-64087600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:64082600-64088800	Strong transcription	HepG2	liver
17	chr2:64082600-64089400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:64082800-64085400	Genic enhancers	Fetal Thymus	thymus
19	chr2:64082800-64086400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:64082800-64087400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:64083000-64085400	Strong transcription	Primary B cells from cord blood	blood
22	chr2:64083000-64085600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:64083000-64087000	Strong transcription	A549	lung
24	chr2:64083000-64087600	Strong transcription	Fetal Intestine Large	intestine
25	chr2:64083000-64089400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:64083000-64089600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr2:64083200-64087000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:64083200-64087600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:64083200-64089600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:64083200-64089600	Strong transcription	NH-A	brain
33	chr2:64083200-64090200	Strong transcription	Fetal Muscle Leg	muscle
34	chr2:64083200-64091600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:64083200-64092000	Strong transcription	Fetal Lung	lung
36	chr2:64083200-64097800	Weak transcription	Right Atrium	heart
37	chr2:64083200-64110200	Weak transcription	Small Intestine	intestine
38	chr2:64083200-64110600	Weak transcription	Pancreas	Pancrea
39	chr2:64083400-64087400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:64083400-64088400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr2:64083400-64089600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:64083400-64091600	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr2:64083600-64085800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:64083600-64086400	Strong transcription	Osteobl	bone
45	chr2:64083600-64086600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:64083600-64087200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:64083600-64087600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr2:64083600-64088400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:64083600-64088400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:64083600-64088800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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