Variant report

Variant	rs7228684
Chromosome Location	chr18:13052473-13052474
allele	A/C
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	FOS	chr18:13051895-13052515	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr18:13052069-13052517	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13030155..13031779-chr18:13051072..13053122,2	K562	blood:
2	chr18:13045915..13049710-chr18:13050964..13055431,5	K562	blood:

Variant related genes	Relation type
CEP192	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10163827	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11080617	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11080618	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11659979	0.82[CHB][hapmap]
rs11661559	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11661908	0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs11662634	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11662766	0.87[JPT][hapmap]
rs11664213	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11664469	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12327306	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12604538	0.86[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap]
rs12605267	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12607398	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12607919	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs12953783	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12957380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12960349	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12961596	0.95[ASN][1000 genomes]
rs12963426	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12970503	0.95[ASN][1000 genomes]
rs12970508	0.87[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap]
rs12971036	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12971069	0.81[AMR][1000 genomes]
rs13381134	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13381779	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523064	0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs17603207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17659689	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17659749	0.93[ASN][1000 genomes]
rs17659896	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2015763	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2282540	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2282541	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28551661	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28654613	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34117444	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34166083	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34302481	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35368962	0.94[ASN][1000 genomes]
rs35563947	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809914	0.86[ASN][1000 genomes]
rs3976787	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.95[ASN][1000 genomes]
rs496270	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56263236	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6505772	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs68004799	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71353241	0.85[EUR][1000 genomes]
rs7229869	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7230391	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7230435	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7234938	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7236710	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7237711	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7239486	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8083393	0.87[JPT][hapmap]
rs8083401	0.88[ASN][1000 genomes]
rs8086882	0.81[ASN][1000 genomes]
rs8089724	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8090667	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs8093236	0.93[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs8093576	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8096860	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8566	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9950241	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7228684	CEP192	cis	Nerve Tibial	GTEx
rs7228684	CEP192	cis	Thyroid	GTEx
rs7228684	CEP192	cis	parietal	SCAN
rs7228684	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs7228684	CEP192	cis	lung	GTEx
rs7228684	CEP192	cis	Esophagus Muscularis	GTEx
rs7228684	CEP192	cis	Artery Tibial	GTEx
rs7228684	CEP192	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13013800-13053200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:13016800-13053200	Weak transcription	Esophagus	oesophagus
3	chr18:13017200-13056000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:13018600-13117400	Weak transcription	Stomach Mucosa	stomach
5	chr18:13032000-13056000	Weak transcription	HSMMtube	muscle
6	chr18:13033400-13053800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:13036800-13053200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr18:13041600-13063600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr18:13041800-13058400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr18:13041800-13064400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr18:13043200-13053200	Weak transcription	Brain Germinal Matrix	brain
12	chr18:13043200-13054000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr18:13043200-13056000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:13043200-13058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:13043200-13058600	Weak transcription	Fetal Heart	heart
16	chr18:13043200-13077800	Strong transcription	Dnd41	blood
17	chr18:13045400-13063800	Strong transcription	Fetal Thymus	thymus
18	chr18:13045600-13053400	Strong transcription	K562	blood
19	chr18:13045600-13062400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr18:13045600-13063200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr18:13045800-13056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr18:13045800-13057000	Strong transcription	A549	lung
23	chr18:13045800-13062400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr18:13045800-13063800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr18:13046000-13057600	Strong transcription	Adipose Nuclei	Adipose
26	chr18:13046000-13058200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr18:13046000-13060600	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr18:13046000-13062200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr18:13046000-13062200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr18:13046000-13062200	Strong transcription	Thymus	Thymus
31	chr18:13046000-13062400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr18:13046000-13062400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr18:13046000-13062400	Strong transcription	Fetal Intestine Large	intestine
34	chr18:13046000-13062400	Strong transcription	Fetal Muscle Leg	muscle
35	chr18:13046000-13062400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr18:13046000-13063400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr18:13046000-13063800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr18:13046000-13063800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr18:13046000-13078600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr18:13046400-13052600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr18:13046400-13052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr18:13046800-13062400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr18:13047200-13055200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr18:13047200-13062200	Strong transcription	Liver	Liver
45	chr18:13047400-13052800	Weak transcription	Ovary	ovary
46	chr18:13047600-13053200	Weak transcription	Spleen	Spleen
47	chr18:13048000-13058800	Strong transcription	Rectal Smooth Muscle	rectum
48	chr18:13048200-13056800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr18:13048200-13057200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr18:13048200-13057800	Strong transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links