Variant report

Variant	rs6688636
Chromosome Location	chr1:155478897-155478898
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	chr1:155477742..155481742-chr1:155532390..155535967,3	MCF-7	breast:
2	chr1:155476586..155479575-chr1:155503974..155506052,2	K562	blood:

Variant related genes	Relation type
ENSG00000116539	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10752611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs10796943	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10796945	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs10796946	0.93[ASN][1000 genomes]
rs10796947	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908463	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10908465	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs10908466	0.93[ASN][1000 genomes]
rs10908467	0.93[ASN][1000 genomes]
rs10908469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs10908471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10908472	0.94[ASN][1000 genomes]
rs10908479	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11264359	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11264361	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11264363	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs11264367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs11264371	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11264372	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11264374	0.93[ASN][1000 genomes]
rs11264375	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs11264380	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs11264381	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs11264383	0.95[ASN][1000 genomes]
rs11264386	0.88[ASN][1000 genomes]
rs11264387	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs11582072	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026638	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs12028416	0.91[ASN][1000 genomes]
rs12030596	0.95[ASN][1000 genomes]
rs12035524	0.91[JPT][hapmap]
rs12037824	0.89[ASN][1000 genomes]
rs12041534	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs12046473	0.87[ASN][1000 genomes]
rs12047756	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12067371	0.93[ASN][1000 genomes]
rs12079134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12131079	0.81[AMR][1000 genomes]
rs12143948	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs12239100	0.93[ASN][1000 genomes]
rs12239114	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12724079	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12744132	0.91[JPT][hapmap]
rs12746592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs1325908	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1360554	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1556488	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1886905	0.92[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs2048431	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2175391	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs2297480	0.89[CHB][hapmap]
rs2666826	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs348196	0.91[JPT][hapmap]
rs35615695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738590	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs3892792	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs475550	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs5005770	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6427278	0.81[ASN][1000 genomes]
rs6684889	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6696888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs678157	0.91[JPT][hapmap]
rs7411786	0.94[ASN][1000 genomes]
rs7556102	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6688636	GBA	cis	Esophagus Mucosa	GTEx
rs6688636	YY1AP1	cis	cerebellum	SCAN
rs6688636	PRUNE	cis	cerebellum	SCAN
rs6688636	GBAP1	cis	Artery Tibial	GTEx
rs6688636	THEM5	cis	parietal	SCAN
rs6688636	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs6688636	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs6688636	S100A8	cis	cerebellum	SCAN
rs6688636	C1orf56	cis	parietal	SCAN
rs6688636	HDGF	cis	parietal	SCAN
rs6688636	GBAP1	cis	parietal	SCAN
rs6688636	BCAN	cis	cerebellum	SCAN
rs6688636	YY1AP1	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155450000-155483000	Weak transcription	NHLF	lung
2	chr1:155452000-155488800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155452200-155481400	Weak transcription	Thymus	Thymus
4	chr1:155452200-155482400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:155452400-155483000	Weak transcription	HSMM	muscle
6	chr1:155452400-155505200	Weak transcription	Placenta	Placenta
7	chr1:155457800-155482400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:155462800-155497400	Weak transcription	Pancreas	Pancrea
9	chr1:155463000-155489400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:155464800-155488800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:155466600-155500600	Weak transcription	Aorta	Aorta
12	chr1:155470200-155482000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:155470200-155490800	Weak transcription	NHEK	skin
14	chr1:155470400-155481000	Weak transcription	Hela-S3	cervix
15	chr1:155470400-155483000	Weak transcription	NHDF-Ad	bronchial
16	chr1:155470400-155488800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:155470400-155489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:155470400-155492000	Weak transcription	NH-A	brain
19	chr1:155470400-155495000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:155470400-155501400	Weak transcription	Fetal Kidney	kidney
21	chr1:155470600-155481200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:155470600-155481400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:155470600-155481400	Weak transcription	Fetal Intestine Large	intestine
24	chr1:155470600-155481400	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:155470600-155481400	Weak transcription	Fetal Stomach	stomach
26	chr1:155470600-155484200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:155470600-155488600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:155470600-155488800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:155470600-155488800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:155470600-155489400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:155470600-155489400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:155470600-155492600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:155470600-155493200	Weak transcription	Small Intestine	intestine
34	chr1:155470600-155498600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:155470800-155493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:155471000-155479600	Weak transcription	Fetal Brain Male	brain
37	chr1:155471200-155482400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:155471200-155498800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:155471400-155483000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:155471400-155489400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:155471400-155489400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:155471600-155488000	Weak transcription	Primary B cells from cord blood	blood
43	chr1:155473800-155482000	Weak transcription	Left Ventricle	heart
44	chr1:155473800-155482600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:155473800-155488600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:155474000-155488600	Weak transcription	A549	lung
47	chr1:155474200-155501400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:155475400-155483200	Weak transcription	K562	blood
49	chr1:155476200-155483400	Strong transcription	Fetal Intestine Small	intestine
50	chr1:155476400-155518200	Weak transcription	HMEC	breast

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