Variant report

Variant	rs4538187
Chromosome Location	chr2:64103741-64103742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:64101796..64104187-chr2:64117437..64118984,2	MCF-7	breast:
2	chr2:63905199..63906853-chr2:64102018..64104600,2	MCF-7	breast:
3	chr2:64101527..64104952-chr2:64106115..64108831,3	MCF-7	breast:
4	chr2:64095211..64099085-chr2:64100038..64104293,5	K562	blood:
5	chr2:64066124..64069765-chr2:64101066..64104026,3	K562	blood:

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

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];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865344	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs11558741	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674020	0.93[AFR][1000 genomes];0.94[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	0.83[AFR][1000 genomes];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];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.94[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	0.81[AFR][1000 genomes];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]
rs12991311	0.92[YRI][hapmap]
rs12996866	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006124	0.92[YRI][hapmap]
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	0.93[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]
rs17619717	0.85[YRI][hapmap]
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];1.00[YRI][hapmap];0.83[AFR][1000 genomes];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];0.91[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[AFR][1000 genomes];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]
rs4671071	0.90[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];0.83[YRI][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];0.91[YRI][hapmap];0.91[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];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546031	0.82[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];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546033	0.85[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]
rs6710230	0.92[YRI][hapmap]
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];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726257	0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs67308158	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731508	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732746	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]
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];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67615384	0.87[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];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597935	0.83[MKK][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4538187	UGP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64078000-64108000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:64082200-64110000	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:64083000-64123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:64083000-64129200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:64083200-64110200	Weak transcription	Small Intestine	intestine
6	chr2:64083200-64110600	Weak transcription	Pancreas	Pancrea
7	chr2:64086600-64110000	Weak transcription	Esophagus	oesophagus
8	chr2:64088000-64107800	Weak transcription	Colonic Mucosa	Colon
9	chr2:64091400-64110000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:64091800-64107800	Weak transcription	Brain Germinal Matrix	brain
11	chr2:64093000-64106400	Strong transcription	Fetal Thymus	thymus
12	chr2:64093800-64107600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:64093800-64109200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:64093800-64110000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:64094000-64107800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:64094000-64109400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:64094000-64110800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:64098600-64106000	Strong transcription	Primary T cells from cord blood	blood
19	chr2:64099000-64105800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:64099400-64106200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr2:64099600-64105400	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr2:64100000-64106400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:64101200-64103800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:64101200-64105400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:64101200-64105600	Strong transcription	HSMM	muscle
26	chr2:64101200-64107600	Weak transcription	NH-A	brain
27	chr2:64101200-64113600	Weak transcription	Fetal Stomach	stomach
28	chr2:64101400-64103800	Enhancers	Brain Hippocampus Middle	brain
29	chr2:64101400-64104000	Enhancers	Fetal Brain Male	brain
30	chr2:64101400-64104200	Weak transcription	Placenta	Placenta
31	chr2:64101400-64104800	Genic enhancers	Fetal Heart	heart
32	chr2:64101400-64110000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:64101400-64110600	Weak transcription	HUVEC	blood vessel
34	chr2:64101600-64103800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:64101600-64104000	Enhancers	Brain Substantia Nigra	brain
36	chr2:64101600-64104400	Enhancers	HMEC	breast
37	chr2:64101600-64104600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:64101600-64106000	Strong transcription	Primary B cells from cord blood	blood
39	chr2:64101600-64106000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:64101600-64106200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:64101600-64108800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
42	chr2:64101600-64109400	Weak transcription	Fetal Intestine Large	intestine
43	chr2:64101600-64110000	Weak transcription	NHLF	lung
44	chr2:64101800-64103800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:64101800-64103800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr2:64101800-64104200	Strong transcription	Liver	Liver
47	chr2:64101800-64105000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:64101800-64106600	Strong transcription	Dnd41	blood
49	chr2:64101800-64110000	Weak transcription	Fetal Lung	lung
50	chr2:64101800-64110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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