Variant report

Variant	rs34645929
Chromosome Location	chr12:66530032-66530033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66524156..66526085-chr12:66529096..66530644,2	K562	blood:
2	chr12:66523605..66525489-chr12:66527409..66530193,2	MCF-7	breast:
3	chr12:66529650..66532056-chr12:66539532..66541211,2	MCF-7	breast:
4	chr12:66524156..66526872-chr12:66529144..66534313,4	K562	blood:

Variant related genes	Relation type
ENSG00000239335	Chromatin interaction
ENSG00000139233	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10400539	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10506478	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878381	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878382	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878383	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878389	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878391	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176043	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11176054	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176056	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176063	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11176065	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176067	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176068	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11176080	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11176082	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12227630	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12832926	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767200	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882201	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898304	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1921083	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141709	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178486	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870781	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34755483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474482	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4575321	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56271210	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61927092	0.83[ASN][1000 genomes]
rs7295147	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302893	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7305938	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966453	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7966561	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7979029	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979775	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899214	chr12:66516692-66556960	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv1009248	chr12:66525948-66530263	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv2607781	chr12:66526818-66530397	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3488297	chr12:66527270-66530148	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	esv3529632	chr12:66527309-66530299	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv8872	chr12:66527383-66530133	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2318656	chr12:66527471-66530119	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv498795	chr12:66527635-66530378	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34645929	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs34645929	RP11-745O10.2	cis	Artery Tibial	GTEx
rs34645929	RP11-745O10.2	cis	lung	GTEx
rs34645929	RP11-745O10.2	cis	Thyroid	GTEx
rs34645929	RP11-745O10.2	cis	Whole Blood	GTEx
rs34645929	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66525000-66531200	Weak transcription	Lung	lung
2	chr12:66525000-66533200	Weak transcription	Gastric	stomach
3	chr12:66525200-66533200	Weak transcription	Esophagus	oesophagus
4	chr12:66525200-66533200	Weak transcription	Pancreas	Pancrea
5	chr12:66525200-66534400	Weak transcription	Small Intestine	intestine
6	chr12:66525400-66530200	Weak transcription	Ovary	ovary
7	chr12:66525400-66533200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:66525400-66533200	Weak transcription	Spleen	Spleen
9	chr12:66525400-66533400	Weak transcription	Aorta	Aorta
10	chr12:66525400-66533400	Weak transcription	Fetal Brain Male	brain
11	chr12:66525400-66534400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:66525400-66562400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:66525600-66531800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:66525600-66533200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:66525600-66533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:66525600-66533400	Weak transcription	Brain Substantia Nigra	brain
17	chr12:66525600-66533600	Weak transcription	Right Ventricle	heart
18	chr12:66525600-66536000	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:66525600-66536400	Weak transcription	Stomach Mucosa	stomach
20	chr12:66525600-66549000	Weak transcription	Colonic Mucosa	Colon
21	chr12:66525600-66552400	Weak transcription	Brain Angular Gyrus	brain
22	chr12:66525600-66561800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:66525800-66532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:66525800-66533400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:66526000-66533400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:66526200-66534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:66526400-66533200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:66526400-66536000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr12:66526600-66530200	Weak transcription	Left Ventricle	heart
30	chr12:66526600-66530400	Weak transcription	NHLF	lung
31	chr12:66526600-66533200	Weak transcription	Fetal Stomach	stomach
32	chr12:66526600-66533200	Weak transcription	Thymus	Thymus
33	chr12:66526600-66534400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr12:66526600-66534400	Weak transcription	HepG2	liver
35	chr12:66526600-66557200	Weak transcription	Psoas Muscle	Psoas
36	chr12:66526800-66531000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:66526800-66531400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:66526800-66531400	Weak transcription	HSMMtube	muscle
39	chr12:66526800-66531400	Weak transcription	NHDF-Ad	bronchial
40	chr12:66526800-66533200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:66526800-66533200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:66526800-66538600	Weak transcription	Hela-S3	cervix
43	chr12:66527000-66531800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:66527000-66531800	Weak transcription	HMEC	breast
45	chr12:66527000-66533200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:66527000-66554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:66527200-66533200	Weak transcription	Fetal Intestine Small	intestine
48	chr12:66527400-66533200	Weak transcription	Fetal Heart	heart
49	chr12:66529800-66530800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:66529800-66532000	Strong transcription	NHEK	skin

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