Variant report

Variant	rs12360114
Chromosome Location	chr10:54789631-54789632
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10508984	0.90[EUR][1000 genomes]
rs10740531	0.89[EUR][1000 genomes]
rs10824852	0.94[JPT][hapmap];0.81[MEX][hapmap]
rs10824856	0.89[EUR][1000 genomes]
rs10824857	0.92[EUR][1000 genomes]
rs10824859	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10824860	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11003335	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11003336	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11003339	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11003340	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11003341	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11003343	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11812875	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11819148	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1539513	0.94[JPT][hapmap]
rs1917190	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1917194	0.90[EUR][1000 genomes]
rs1917195	0.90[EUR][1000 genomes]
rs1917196	0.90[EUR][1000 genomes]
rs1917197	0.90[EUR][1000 genomes]
rs1917205	0.88[EUR][1000 genomes]
rs1949813	0.90[EUR][1000 genomes]
rs1949814	0.90[EUR][1000 genomes]
rs2248319	0.88[EUR][1000 genomes]
rs2248678	0.88[EUR][1000 genomes]
rs2253152	0.90[EUR][1000 genomes]
rs2253266	0.90[EUR][1000 genomes]
rs2253468	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2264663	0.90[EUR][1000 genomes]
rs2265880	0.88[EUR][1000 genomes]
rs2462479	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2492354	0.82[EUR][1000 genomes]
rs2891425	0.94[JPT][hapmap]
rs2891426	0.83[EUR][1000 genomes]
rs7069155	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7092980	0.89[JPT][hapmap];0.81[MEX][hapmap]
rs72800376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72800377	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv895405	chr10:54765608-54824741	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv508585	chr10:54769376-54796804	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv895406	chr10:54780677-54830687	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv3523695	chr10:54782396-54790044	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3509840	chr10:54782746-54790644	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3523693	chr10:54782796-54789894	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	esv1821304	chr10:54784919-54794208	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv1828095	chr10:54784919-54794208	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv1851757	chr10:54784919-54794208	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv3508729	chr10:54784971-54789819	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	esv3510951	chr10:54784971-54789819	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv437674	chr10:54787062-54793330	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv437675	chr10:54787838-54793330	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv437676	chr10:54787838-54793330	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12360114	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54785200-54789800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr10:54785400-54789800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:54785600-54789800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr10:54785800-54789800	Weak transcription	Fetal Lung	lung
5	chr10:54786000-54789800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:54786000-54790400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:54789000-54790000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:54789000-54790200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr10:54789200-54789800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:54789200-54789800	Enhancers	Esophagus	oesophagus
11	chr10:54789200-54790000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:54789200-54790200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:54789200-54791000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:54789200-54791000	Enhancers	Placenta	Placenta
15	chr10:54789200-54791200	Enhancers	Fetal Intestine Large	intestine
16	chr10:54789200-54792000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr10:54789400-54789800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:54789400-54789800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:54789400-54789800	Active TSS	Stomach Mucosa	stomach
20	chr10:54789400-54790000	Enhancers	Pancreas	Pancrea
21	chr10:54789400-54790200	Active TSS	Fetal Stomach	stomach
22	chr10:54789400-54791000	Enhancers	GM12878-XiMat	blood
23	chr10:54789400-54791000	Enhancers	HepG2	liver
24	chr10:54789400-54791000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr10:54789400-54791200	Enhancers	Primary hematopoietic stem cells	blood
26	chr10:54789400-54791200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr10:54789400-54791200	Enhancers	NHEK	skin
28	chr10:54789600-54789800	Enhancers	Lung	lung
29	chr10:54789600-54790000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr10:54789600-54790000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr10:54789600-54790000	Flanking Active TSS	HUVEC	blood vessel
32	chr10:54789600-54790200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:54789600-54790600	Enhancers	Hela-S3	cervix
34	chr10:54789600-54790800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr10:54789600-54790800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr10:54789600-54790800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr10:54789600-54790800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr10:54789600-54790800	Flanking Active TSS	Fetal Kidney	kidney
39	chr10:54789600-54791000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr10:54789600-54791000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:54789600-54791000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr10:54789600-54791000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr10:54789600-54791000	Enhancers	Duodenum Mucosa	Duodenum
44	chr10:54789600-54791200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr10:54789600-54791400	Enhancers	Fetal Intestine Small	intestine

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