Variant report

Variant	rs1787004
Chromosome Location	chr18:13131395-13131396
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:13124233..13126010-chr18:13129729..13132355,2	K562	blood:
2	chr18:13130413..13132086-chr18:13135033..13137817,2	MCF-7	breast:
3	chr18:13128234..13129969-chr18:13130472..13133331,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10221326	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10221384	0.89[CEU][hapmap];0.86[MEX][hapmap]
rs11080620	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11663049	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs12605638	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12954256	0.92[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap]
rs12955780	0.88[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1474043	0.92[CEU][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs1786263	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1786270	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1786279	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1787000	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787003	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1787008	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1973779	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28619103	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28641764	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2902856	0.94[CHD][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35790309	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3809912	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs472702	0.92[CEU][hapmap];0.86[MEX][hapmap]
rs472992	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs473580	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs474337	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs475139	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs478006	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4797730	0.91[YRI][hapmap]
rs482360	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs482577	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs490853	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs491349	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492458	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs492723	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498685	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs518145	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs527839	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs529620	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs529954	1.00[YRI][hapmap]
rs547084	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs554719	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs554854	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556371	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs556536	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs557846	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs562151	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs565832	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs567031	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs569453	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs570505	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs576963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs578208	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6505775	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6505776	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6505777	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6505780	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs692833	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs692964	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71353243	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7226616	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7229870	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7233600	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7233814	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7234094	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7234960	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7236162	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236764	0.81[AMR][1000 genomes]
rs7237236	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7241536	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7243660	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8088313	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8089123	0.92[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs8097038	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8097125	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9783859	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9783903	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9949589	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9949682	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs9958369	0.81[AMR][1000 genomes]
rs9961669	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9964466	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv515878	chr18:13122618-13142415	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv817785	chr18:13130681-13133577	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1787004	CEP192	cis	Esophagus Mucosa	GTEx
rs1787004	CEP192	cis	Nerve Tibial	GTEx
rs1787004	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs1787004	CEP192	cis	Whole Blood	GTEx
rs1787004	CEP192	cis	Thyroid	GTEx
rs1787004	CEP192	cis	parietal	SCAN
rs1787004	CEP192	cis	cerebellum	SCAN
rs1787004	CEP192	cis	Liver	GTEx
rs1787004	CEP192	cis	Heart Left Ventricle	GTEx
rs1787004	CEP192	cis	Brain Pons	GTEx
rs1787004	CEP192	cis	Artery Tibial	GTEx
rs1787004	CEP192	cis	Adipose Subcutaneous	GTEx
rs1787004	CEP192	cis	Temporal Cortex	GTEx
rs1787004	CEP192	cis	lung	GTEx
rs1787004	CEP192	cis	multi-tissue	Pritchard
rs1787004	CEP192	cis	Artery Aorta	GTEx
rs1787004	CEP192	cis	Frontal Cortex	GTEx
rs1787004	CEP192	cis	Esophagus Muscularis	GTEx
rs1787004	CEP192	cis	Stomach	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13106800-13135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:13118200-13132600	Weak transcription	HepG2	liver
3	chr18:13118400-13135600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr18:13118400-13136200	Weak transcription	Psoas Muscle	Psoas
5	chr18:13118800-13136800	Weak transcription	HSMMtube	muscle
6	chr18:13119000-13133400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr18:13119000-13134200	Weak transcription	Fetal Lung	lung
8	chr18:13119000-13136400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr18:13119200-13135800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr18:13119200-13136400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr18:13119400-13133600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr18:13119600-13135400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr18:13121200-13136400	Weak transcription	NHDF-Ad	bronchial
14	chr18:13121400-13134000	Weak transcription	HMEC	breast
15	chr18:13121400-13136600	Weak transcription	Brain Angular Gyrus	brain
16	chr18:13121600-13131600	Weak transcription	Fetal Kidney	kidney
17	chr18:13121600-13135800	Weak transcription	Fetal Brain Male	brain
18	chr18:13121600-13136000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr18:13121800-13134200	Weak transcription	HUVEC	blood vessel
20	chr18:13121800-13136400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr18:13122000-13136400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr18:13123800-13136400	Weak transcription	HSMM	muscle
23	chr18:13124800-13131400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr18:13125600-13135800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr18:13126600-13135000	Weak transcription	Ovary	ovary
26	chr18:13126800-13133400	Weak transcription	K562	blood
27	chr18:13127000-13133400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr18:13127000-13135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr18:13127000-13136200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr18:13127000-13136200	Weak transcription	Placenta	Placenta
31	chr18:13127200-13135800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr18:13127200-13136200	Weak transcription	Brain Anterior Caudate	brain
33	chr18:13127400-13132000	Weak transcription	Fetal Intestine Large	intestine
34	chr18:13127400-13132000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr18:13127400-13134200	Weak transcription	NHEK	skin
36	chr18:13127400-13135600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr18:13127400-13135800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr18:13127400-13135800	Weak transcription	GM12878-XiMat	blood
39	chr18:13127400-13136400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr18:13127600-13132400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr18:13127600-13132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr18:13127600-13133200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr18:13127600-13134800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr18:13127600-13135200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr18:13127600-13135400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:13127600-13135600	Weak transcription	Fetal Brain Female	brain
47	chr18:13127600-13135800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr18:13127600-13135800	Weak transcription	Left Ventricle	heart
49	chr18:13127600-13135800	Weak transcription	Thymus	Thymus
50	chr18:13127600-13136000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links