Variant report

Variant	rs1474043
Chromosome Location	chr18:12951738-12951739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12726304..12729223-chr18:12948825..12951791,2	K562	blood:
2	chr18:12944429..12952802-chr18:12987284..12998193,21	K562	blood:
3	chr18:12950305..12952653-chr18:12960461..12963058,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266969	Chromatin interaction
ENSG00000101639	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10221326	0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10221384	0.89[CEU][hapmap];0.82[MEX][hapmap]
rs11080620	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11663049	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12605638	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12954256	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12955780	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1786263	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes]
rs1786270	0.88[AMR][1000 genomes]
rs1787000	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs1787003	0.86[AMR][1000 genomes]
rs1787008	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1973779	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28619103	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28641764	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2902856	1.00[ASW][hapmap];0.85[CEU][hapmap];0.80[GIH][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35790309	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3809912	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs472702	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs472992	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs473580	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs474337	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs478006	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs490853	0.88[AMR][1000 genomes]
rs498685	0.84[CEU][hapmap]
rs4995995	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518145	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs527839	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs529620	0.88[AMR][1000 genomes]
rs547084	0.83[AMR][1000 genomes]
rs554719	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs554854	0.89[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes]
rs556371	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs556536	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs562151	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs565832	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs567031	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs569453	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs570505	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs576963	0.92[CEU][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs578208	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6505775	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6505776	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6505777	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6505780	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs692964	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7226616	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7229870	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7233600	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7233814	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7234094	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7234960	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7236764	0.83[AMR][1000 genomes]
rs7237236	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7241536	0.92[CHB][hapmap];1.00[YRI][hapmap]
rs7243660	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8088313	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8089123	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8097038	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8097125	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9783859	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9783903	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9948139	0.86[AMR][1000 genomes]
rs9948681	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9949589	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9949682	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap]
rs9951698	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9958369	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9961669	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9964466	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9965977	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	esv3450694	chr18:12933001-12955144	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs1474043	CEP192	cis	Brain Pons	GTEx
rs1474043	CEP192	cis	Thyroid	GTEx
rs1474043	CEP192	cis	multi-tissue	Pritchard
rs1474043	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs1474043	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs1474043	CEP192	cis	Esophagus Muscularis	GTEx
rs1474043	CEP192	cis	Nerve Tibial	GTEx
rs1474043	SEH1L	cis	parietal	SCAN
rs1474043	CEP192	cis	Whole Blood	GTEx
rs1474043	CEP192	cis	Artery Tibial	GTEx
rs1474043	CEP192	cis	Adipose Subcutaneous	GTEx
rs1474043	CEP192	cis	Temporal Cortex	GTEx
rs1474043	CEP192	cis	Esophagus Mucosa	GTEx
rs1474043	CEP192	cis	Artery Aorta	GTEx
rs1474043	CEP192	cis	parietal	SCAN
rs1474043	CEP192	cis	cerebellum	SCAN
rs1474043	CEP192	cis	Stomach	GTEx
rs1474043	CEP192	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12951800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr18:12948800-12953400	Weak transcription	HUVEC	blood vessel
3	chr18:12948800-12954400	Weak transcription	NHDF-Ad	bronchial
4	chr18:12948800-12957600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr18:12948800-12958200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr18:12948800-12958200	Weak transcription	Left Ventricle	heart
7	chr18:12948800-12958400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr18:12948800-12958400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr18:12948800-12963200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:12948800-12963200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr18:12948800-12963200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr18:12948800-12963200	Weak transcription	Colon Smooth Muscle	Colon
13	chr18:12948800-12963600	Weak transcription	Esophagus	oesophagus
14	chr18:12948800-12971000	Weak transcription	Ovary	ovary
15	chr18:12948800-12971600	Weak transcription	Pancreas	Pancrea
16	chr18:12948800-12976600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr18:12949000-12952400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr18:12949000-12952400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr18:12949000-12952600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr18:12949000-12953000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr18:12949000-12953000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr18:12949000-12953200	Weak transcription	NH-A	brain
24	chr18:12949000-12953800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr18:12949000-12954600	Weak transcription	HSMMtube	muscle
26	chr18:12949000-12957400	Weak transcription	Fetal Lung	lung
27	chr18:12949000-12957400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr18:12949000-12957600	Weak transcription	Brain Angular Gyrus	brain
29	chr18:12949000-12957600	Weak transcription	Fetal Kidney	kidney
30	chr18:12949000-12963200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr18:12949000-12963200	Weak transcription	NHLF	lung
32	chr18:12949000-12971600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr18:12949000-12975400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr18:12949200-12951800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr18:12949200-12952200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr18:12949200-12953200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr18:12949200-12954200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr18:12949200-12954800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:12949200-12957200	Weak transcription	Adipose Nuclei	Adipose
40	chr18:12949200-12957200	Weak transcription	Brain Germinal Matrix	brain
41	chr18:12949200-12957400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr18:12949200-12957600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr18:12949200-12958200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr18:12949200-12958200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr18:12949200-12960800	Weak transcription	Fetal Heart	heart
46	chr18:12949200-12960800	Weak transcription	Stomach Mucosa	stomach
47	chr18:12949200-12961000	Weak transcription	Colonic Mucosa	Colon
48	chr18:12949200-12963400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr18:12949200-12963600	Weak transcription	Small Intestine	intestine
50	chr18:12949200-12971600	Weak transcription	Brain Substantia Nigra	brain

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