Variant report

Variant	rs7230435
Chromosome Location	chr18:13003224-13003225
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12990233..12992753-chr18:13003201..13005792,2	MCF-7	breast:
2	chr18:12962926..12965519-chr18:13001334..13004209,2	K562	blood:
3	chr18:12988481..12994468-chr18:12998354..13003992,8	MCF-7	breast:
4	chr18:12996926..12999710-chr18:13000576..13003531,2	K562	blood:
5	chr18:13003140..13003705-chr18:13793544..13794119,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101639	Chromatin interaction
ENSG00000266969	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10163827	0.81[ASN][1000 genomes]
rs11080617	0.85[ASN][1000 genomes]
rs11080618	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11661322	0.84[EUR][1000 genomes]
rs11661908	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11662634	0.81[ASN][1000 genomes]
rs11664213	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11664469	0.85[ASN][1000 genomes]
rs12605267	0.85[ASN][1000 genomes]
rs12607398	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12607919	0.86[EUR][1000 genomes]
rs12960349	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12961596	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12963426	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12970503	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12971069	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13381779	0.81[ASN][1000 genomes]
rs1523064	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17659689	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17659749	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17659896	0.87[ASN][1000 genomes]
rs2015763	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282541	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28551661	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28654613	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34166083	0.83[ASN][1000 genomes]
rs34302481	0.87[ASN][1000 genomes]
rs35368962	0.83[ASN][1000 genomes]
rs35563947	0.87[ASN][1000 genomes]
rs3809914	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3976787	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4499304	0.87[EUR][1000 genomes]
rs56263236	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58871601	0.86[EUR][1000 genomes]
rs68004799	0.83[ASN][1000 genomes]
rs7228684	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7229869	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7230391	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7234163	0.87[EUR][1000 genomes]
rs7236710	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7237711	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8083401	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8086882	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8089724	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8090667	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8092888	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8093236	0.84[EUR][1000 genomes]
rs8093576	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8096860	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8566	0.83[ASN][1000 genomes]
rs9950241	0.85[EUR][1000 genomes];0.86[ASN][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	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	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7230435	CEP192	cis	Esophagus Muscularis	GTEx
rs7230435	CEP192	cis	lung	GTEx
rs7230435	CEP192	cis	Artery Tibial	GTEx
rs7230435	CEP192	cis	Esophagus Mucosa	GTEx
rs7230435	CEP192	cis	Nerve Tibial	GTEx
rs7230435	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs7230435	CEP192	cis	Whole Blood	GTEx
rs7230435	CEP192	cis	Adipose Subcutaneous	GTEx
rs7230435	CEP192	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12992000-13004400	Weak transcription	Esophagus	oesophagus
2	chr18:12992200-13004800	Weak transcription	Aorta	Aorta
3	chr18:12992400-13004400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr18:12992800-13004000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr18:12992800-13008800	Weak transcription	Colonic Mucosa	Colon
7	chr18:12992800-13009200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr18:12992800-13013200	Weak transcription	Fetal Kidney	kidney
9	chr18:12992800-13016000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr18:12993000-13006400	Weak transcription	Fetal Brain Female	brain
11	chr18:12993000-13023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:12993200-13004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr18:12993200-13004800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr18:12993200-13006800	Weak transcription	HSMMtube	muscle
15	chr18:12993200-13007000	Weak transcription	Brain Substantia Nigra	brain
16	chr18:12993200-13008400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr18:12993200-13008400	Weak transcription	Osteobl	bone
18	chr18:12993200-13008800	Weak transcription	NHLF	lung
19	chr18:12993400-13003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr18:12993400-13006200	Weak transcription	NH-A	brain
21	chr18:12993400-13006600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:12993400-13008200	Weak transcription	Brain Angular Gyrus	brain
23	chr18:12993400-13017800	Weak transcription	Stomach Mucosa	stomach
24	chr18:12993600-13003600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr18:12993600-13011800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:12993600-13011800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr18:12993800-13003600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr18:12993800-13004000	Weak transcription	NHEK	skin
29	chr18:12993800-13005000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr18:12993800-13008400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr18:12993800-13008400	Weak transcription	Psoas Muscle	Psoas
32	chr18:12993800-13008400	Weak transcription	HMEC	breast
33	chr18:12993800-13008800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr18:12993800-13009200	Weak transcription	NHDF-Ad	bronchial
35	chr18:12994000-13006000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr18:12995000-13011400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr18:12995200-13042000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:12996600-13003600	Weak transcription	Fetal Intestine Small	intestine
39	chr18:12996800-13004800	Weak transcription	Spleen	Spleen
40	chr18:12997000-13004400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr18:12997000-13004400	Weak transcription	Gastric	stomach
42	chr18:12997000-13006600	Weak transcription	Brain Hippocampus Middle	brain
43	chr18:12997000-13008200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr18:12997000-13008600	Weak transcription	Brain Anterior Caudate	brain
45	chr18:12997000-13008800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr18:12997200-13003800	Weak transcription	Left Ventricle	heart
47	chr18:12997200-13006800	Weak transcription	Right Atrium	heart
48	chr18:12997200-13011200	Weak transcription	Right Ventricle	heart
49	chr18:12997200-13013200	Weak transcription	Small Intestine	intestine
50	chr18:12997400-13003600	Weak transcription	Fetal Heart	heart

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