Variant report

Variant	rs12961596
Chromosome Location	chr18:12969749-12969750
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12948345..12951130-chr18:12969418..12973863,3	K562	blood:

Variant related genes	Relation type
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10163827	0.91[ASN][1000 genomes]
rs11080617	0.99[ASN][1000 genomes]
rs11080618	0.97[ASN][1000 genomes]
rs11661908	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11662634	0.91[ASN][1000 genomes]
rs11664213	0.97[ASN][1000 genomes]
rs11664469	0.95[ASN][1000 genomes]
rs12605267	0.99[ASN][1000 genomes]
rs12607398	0.97[ASN][1000 genomes]
rs12607919	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12953783	0.89[ASN][1000 genomes]
rs12957380	0.87[ASN][1000 genomes]
rs12960349	0.97[ASN][1000 genomes]
rs12963426	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12970503	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381779	0.91[ASN][1000 genomes]
rs1523064	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17603207	0.89[ASN][1000 genomes]
rs17659689	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17659749	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17659896	0.97[ASN][1000 genomes]
rs2015763	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282540	0.87[ASN][1000 genomes]
rs2282541	0.90[ASN][1000 genomes]
rs28551661	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28654613	0.96[ASN][1000 genomes]
rs34166083	0.97[ASN][1000 genomes]
rs34302481	0.97[ASN][1000 genomes]
rs35368962	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35563947	0.97[ASN][1000 genomes]
rs3809914	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3976787	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56263236	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs68004799	0.97[ASN][1000 genomes]
rs7228684	0.95[ASN][1000 genomes]
rs7229869	0.84[ASN][1000 genomes]
rs7230391	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7230435	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7234938	0.87[ASN][1000 genomes]
rs7236710	0.81[ASN][1000 genomes]
rs7237711	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7239486	0.90[ASN][1000 genomes]
rs8083401	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8086882	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8089724	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8090667	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8092888	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8093236	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8093576	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8096860	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8566	0.97[ASN][1000 genomes]
rs9950241	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12961596	CEP192	cis	lung	GTEx
rs12961596	CEP192	cis	Artery Tibial	GTEx
rs12961596	CEP192	cis	Nerve Tibial	GTEx
rs12961596	CEP192	cis	Esophagus Muscularis	GTEx
rs12961596	CEP192	cis	Adipose Subcutaneous	GTEx
rs12961596	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs12961596	CEP192	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12971000	Weak transcription	Ovary	ovary
2	chr18:12948800-12971600	Weak transcription	Pancreas	Pancrea
3	chr18:12948800-12976600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr18:12949000-12971600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr18:12949000-12975400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr18:12949200-12971600	Weak transcription	Brain Substantia Nigra	brain
8	chr18:12949200-12972000	Weak transcription	Right Ventricle	heart
9	chr18:12949200-12989400	Weak transcription	Psoas Muscle	Psoas
10	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
11	chr18:12951400-12971800	Weak transcription	Gastric	stomach
12	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr18:12951600-12988200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr18:12951800-12978400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr18:12953200-12979000	Strong transcription	Fetal Thymus	thymus
16	chr18:12956200-12975800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr18:12957400-12978400	Strong transcription	Dnd41	blood
18	chr18:12959000-12971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr18:12959000-12972000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr18:12959000-12990200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr18:12959200-12970800	Weak transcription	Brain Germinal Matrix	brain
22	chr18:12959200-12971600	Weak transcription	Brain Angular Gyrus	brain
23	chr18:12959200-12978200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr18:12960400-12972400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr18:12961000-12978400	Strong transcription	Fetal Intestine Small	intestine
26	chr18:12961200-12975400	Weak transcription	Stomach Mucosa	stomach
27	chr18:12961400-12975600	Weak transcription	Right Atrium	heart
28	chr18:12961600-12971800	Weak transcription	Aorta	Aorta
29	chr18:12961600-12975400	Weak transcription	Fetal Heart	heart
30	chr18:12962200-12974000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr18:12962800-12975800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:12963200-12978600	Strong transcription	Fetal Intestine Large	intestine
33	chr18:12963600-12978600	Strong transcription	Fetal Stomach	stomach
34	chr18:12964000-12969800	Weak transcription	Primary B cells from cord blood	blood
35	chr18:12964000-12970400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr18:12964000-12970600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr18:12964000-12971000	Weak transcription	Fetal Lung	lung
38	chr18:12964000-12971000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr18:12964000-12971000	Weak transcription	Spleen	Spleen
40	chr18:12964000-12971600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr18:12964000-12971600	Weak transcription	Brain Anterior Caudate	brain
42	chr18:12964000-12971800	Weak transcription	Brain Hippocampus Middle	brain
43	chr18:12964000-12971800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr18:12964000-12971800	Weak transcription	Small Intestine	intestine
45	chr18:12964000-12972000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr18:12964000-12972200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:12964000-12975400	Weak transcription	Colonic Mucosa	Colon
48	chr18:12964200-12970200	Weak transcription	NH-A	brain
49	chr18:12964200-12971400	Weak transcription	Placenta	Placenta
50	chr18:12964200-12971600	Weak transcription	NHLF	lung

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