Variant report

Variant	rs9628662
Chromosome Location	chr1:155206341-155206342
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	CEBPB	chr1:155206235-155206647	MCF-7	breast:	n/a	chr1:155206434-155206445
2	CEBPB	chr1:155206273-155206559	A549	lung:	n/a	chr1:155206434-155206445
3	CEBPB	chr1:155206296-155206605	IMR90	lung:	n/a	chr1:155206434-155206445
4	CEBPB	chr1:155206261-155206604	Hela-S3	cervix:	n/a	chr1:155206434-155206445
5	CEBPB	chr1:155206311-155206594	A549	lung:	n/a	chr1:155206434-155206445
6	POLR2A	chr1:155202579-155206572	PFSK-1	brain:	n/a	n/a
7	CEBPB	chr1:155206303-155206598	HepG2	liver:	n/a	chr1:155206434-155206445
8	CEBPB	chr1:155206299-155206527	K562	blood:	n/a	chr1:155206434-155206445
9	CEBPB	chr1:155206222-155206628	MCF-7	breast:	n/a	chr1:155206434-155206445
10	CEBPB	chr1:155206294-155206577	K562	blood:	n/a	chr1:155206434-155206445

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155196524..155199471-chr1:155205933..155208728,2	MCF-7	breast:

Variant related genes	Relation type
GBA	TF binding region
ENSG00000160766	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1045253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046188	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1052176	0.82[ASN][1000 genomes]
rs1052177	0.82[ASN][1000 genomes]
rs1076556	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1078699	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10796940	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908459	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264343	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264346	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11264348	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11264349	0.83[ASN][1000 genomes]
rs11264352	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11264353	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11264359	0.85[CHB][hapmap]
rs1142287	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11577338	0.86[ASN][1000 genomes]
rs12026638	0.84[CHB][hapmap]
rs12034326	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042020	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12044063	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12049375	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12406363	0.84[ASN][1000 genomes]
rs12407919	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12563994	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12723761	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12724449	0.85[ASN][1000 genomes]
rs12748155	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12749306	0.85[ASN][1000 genomes]
rs1546818	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1800438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800442	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807042	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2009578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071053	0.82[ASN][1000 genomes]
rs2072647	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2075566	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2075569	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236863	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2236864	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2242576	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2242577	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2297480	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2361536	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2361543	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28373017	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28595322	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3754485	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768566	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814318	0.80[ASN][1000 genomes]
rs3814319	0.82[ASN][1000 genomes]
rs4043	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4620533	0.82[ASN][1000 genomes]
rs56310840	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59352002	0.82[AMR][1000 genomes]
rs734073	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs734074	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs741756	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7520184	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7543234	0.80[AMR][1000 genomes]
rs7549276	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7554780	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs762488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8847	0.82[ASN][1000 genomes]
rs932972	0.82[ASN][1000 genomes]
rs9729564	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
4	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
5	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
6	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
7	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
8	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
9	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
10	nsv870053	chr1:155180349-155212316	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	esv13606	chr1:155180489-155221243	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv1008748	chr1:155189148-155230610	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
13	nsv1011773	chr1:155189148-155234821	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
14	esv1793876	chr1:155194112-155212255	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
15	nsv946412	chr1:155204296-155207961	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv8480	chr1:155206335-155214536	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs9628662	LAMTOR2	cis	lymphoblastoid	seeQTL
rs9628662	GBAP1	cis	Esophagus Mucosa	GTEx
rs9628662	GBAP1	cis	Thyroid	GTEx
rs9628662	GBA	cis	Esophagus Mucosa	GTEx
rs9628662	GBAP1	cis	parietal	SCAN
rs9628662	RP11-263K19.4	cis	Whole Blood	GTEx
rs9628662	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs9628662	GBAP1	cis	cerebellum	SCAN
rs9628662	THEM5	cis	parietal	SCAN
rs9628662	SPRR4	cis	parietal	SCAN
rs9628662	THBS3	cis	lung	GTEx
rs9628662	GBA	cis	lymphoblastoid	seeQTL
rs9628662	THBS3	cis	Whole Blood	GTEx
rs9628662	CRNN	cis	cerebellum	SCAN
rs9628662	GBA///GBAP	Cis_1M	lymphoblastoid	RTeQTL
rs9628662	GBAP1	cis	Artery Tibial	GTEx
rs9628662	GBA	cis	Whole Blood	GTEx
rs9628662	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs9628662	RPRD2	cis	cerebellum	SCAN
rs9628662	EFNA1	cis	cerebellum	SCAN
rs9628662	SNORA42	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155197200-155212800	Weak transcription	Small Intestine	intestine
2	chr1:155198000-155206800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:155198000-155209600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:155198000-155210400	Weak transcription	A549	lung
5	chr1:155198000-155210400	Weak transcription	HMEC	breast
6	chr1:155198000-155210400	Weak transcription	HSMM	muscle
7	chr1:155198000-155210600	Weak transcription	Psoas Muscle	Psoas
8	chr1:155198000-155210800	Weak transcription	Fetal Kidney	kidney
9	chr1:155198200-155207800	Weak transcription	NHLF	lung
10	chr1:155198200-155209600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:155198200-155209600	Weak transcription	Fetal Brain Male	brain
12	chr1:155198200-155210400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:155198200-155210400	Weak transcription	Stomach Mucosa	stomach
14	chr1:155198200-155210400	Weak transcription	NHEK	skin
15	chr1:155198200-155210800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:155198200-155210800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:155201200-155210400	Weak transcription	HepG2	liver
18	chr1:155201400-155210400	Weak transcription	K562	blood
19	chr1:155201400-155210600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:155201800-155210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:155202200-155210400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:155202600-155210400	Weak transcription	Right Atrium	heart
23	chr1:155202800-155210200	Weak transcription	Fetal Lung	lung
24	chr1:155203800-155210400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:155204600-155206800	Strong transcription	Aorta	Aorta
26	chr1:155204600-155209400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:155204600-155209400	Strong transcription	Spleen	Spleen
28	chr1:155204600-155209600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:155204600-155209600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:155204600-155209800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:155204600-155210000	Strong transcription	Fetal Intestine Small	intestine
32	chr1:155204800-155206800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:155204800-155207800	Strong transcription	Esophagus	oesophagus
34	chr1:155204800-155208000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:155204800-155208200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:155204800-155208200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:155204800-155209800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:155205000-155206400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:155205000-155208000	Strong transcription	Liver	Liver
40	chr1:155205000-155208200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:155205000-155209000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:155205000-155209400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:155205000-155209600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:155205000-155209800	Strong transcription	Adipose Nuclei	Adipose
45	chr1:155205000-155209800	Strong transcription	Thymus	Thymus
46	chr1:155205200-155207600	Strong transcription	Fetal Brain Female	brain
47	chr1:155205200-155208000	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:155205200-155208200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:155205200-155208200	Strong transcription	Lung	lung
50	chr1:155205200-155208800	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links