Variant report

Variant	rs2725304
Chromosome Location	chr4:26356875-26356876
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:26356740-26356890	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26353073..26355548-chr4:26356822..26359791,2	K562	blood:

Variant related genes	Relation type
RBPJ	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10805262	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10939111	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11722108	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11722744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11726853	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11727747	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11737637	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12639629	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs12643747	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12648802	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13104136	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13104403	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13108863	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13109703	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13111856	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13114911	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13115260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13116044	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13116873	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13118463	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13119840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13120216	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13125386	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13128014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13128399	0.90[YRI][hapmap]
rs13129276	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13133397	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13134710	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13135156	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13139277	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13139997	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13140860	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13147671	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13152066	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16867798	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2270226	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725303	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2725305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2725325	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28368332	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3109839	0.88[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3109843	0.95[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3109849	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3113016	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3113019	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35142730	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3762930	1.00[YRI][hapmap]
rs4289434	0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4536914	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4692531	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4692532	0.96[CEU][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56795036	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7349722	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7655165	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7656190	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2725304	GBA3	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26323800-26374400	Weak transcription	Lung	lung
2	chr4:26325000-26374200	Weak transcription	Fetal Intestine Large	intestine
3	chr4:26343600-26357200	Weak transcription	Gastric	stomach
4	chr4:26344200-26357400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:26344200-26357800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:26344200-26370800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:26344200-26374200	Weak transcription	Placenta	Placenta
8	chr4:26344400-26357600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:26344800-26368000	Weak transcription	Fetal Intestine Small	intestine
10	chr4:26345000-26357200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:26345200-26362600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:26345400-26357000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:26346400-26357200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:26347600-26357600	Weak transcription	HSMM	muscle
15	chr4:26347800-26362600	Weak transcription	Fetal Lung	lung
16	chr4:26348000-26357200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:26348000-26357200	Weak transcription	Osteobl	bone
18	chr4:26348000-26357400	Weak transcription	NHLF	lung
19	chr4:26348000-26357600	Weak transcription	Adipose Nuclei	Adipose
20	chr4:26348000-26362600	Weak transcription	Fetal Brain Male	brain
21	chr4:26348000-26374400	Weak transcription	Fetal Stomach	stomach
22	chr4:26348200-26357200	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:26348200-26357400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:26348200-26360400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:26349400-26357600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:26349400-26362000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:26350800-26357200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:26351000-26357200	Weak transcription	Pancreas	Pancrea
29	chr4:26351000-26361200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:26351000-26362400	Weak transcription	Right Ventricle	heart
31	chr4:26351000-26374200	Weak transcription	Right Atrium	heart
32	chr4:26351400-26357200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:26351800-26357200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr4:26352400-26357000	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:26352600-26357000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:26352600-26357400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:26353000-26357200	Weak transcription	Primary T cells from cord blood	blood
38	chr4:26353000-26357200	Weak transcription	Fetal Heart	heart
39	chr4:26353200-26357400	Weak transcription	Small Intestine	intestine
40	chr4:26353400-26361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:26353600-26357200	Weak transcription	Brain Angular Gyrus	brain
42	chr4:26353600-26357200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr4:26353800-26357000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:26353800-26357000	Weak transcription	GM12878-XiMat	blood
45	chr4:26354200-26357600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:26354200-26357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:26354200-26359000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:26354400-26357400	Weak transcription	Left Ventricle	heart
49	chr4:26354600-26357200	Weak transcription	HepG2	liver
50	chr4:26355000-26357200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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