Variant report

Variant	rs10875687
Chromosome Location	chr12:48134214-48134215
allele	C/G
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	NFIC	chr12:48133892-48134331	GM12878	blood:	n/a	n/a
2	ELF1	chr12:48133414-48134775	GM12878	blood:	n/a	n/a
3	RUNX3	chr12:48133748-48134302	GM12878	blood:	n/a	n/a
4	MTA3	chr12:48133560-48134651	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:48133625-48134245	GM12892	blood:	n/a	n/a
6	CTCF	chr12:48134100-48134250	GM12874	blood:	n/a	n/a
7	EBF1	chr12:48133826-48134282	GM12878	blood:	n/a	chr12:48134032-48134043 chr12:48134001-48134012
8	CTCF	chr12:48134200-48134350	GM12864	blood:	n/a	n/a
9	ZBTB7A	chr12:48133908-48134269	K562	blood:	n/a	n/a
10	ZNF263	chr12:48133547-48134655	K562	blood:	n/a	n/a
11	POLR2A	chr12:48133458-48135692	ECC-1	luminal epithelium:	n/a	n/a
12	RUNX3	chr12:48133774-48134295	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48133250..48135553-chr12:48296742..48299315,2	K562	blood:
2	chr12:48128880..48137705-chr12:48169546..48175532,12	K562	blood:
3	chr12:48133209..48136160-chr12:48165338..48168109,2	K562	blood:
4	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000111424	Chromatin interaction
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10783212	0.83[ASN][1000 genomes]
rs10875677	0.82[ASN][1000 genomes]
rs10875682	0.81[ASN][1000 genomes]
rs10875685	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875686	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168191	0.81[ASN][1000 genomes]
rs11168192	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs11168193	0.81[ASN][1000 genomes]
rs11168199	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168200	0.94[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168203	0.83[ASN][1000 genomes]
rs11168208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168213	0.80[YRI][hapmap]
rs11168214	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168216	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366410	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12370643	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1541384	0.80[ASN][1000 genomes]
rs2072117	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283346	0.89[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3764013	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61917594	0.80[ASN][1000 genomes]
rs61917595	0.82[ASN][1000 genomes]
rs61917616	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61917617	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580634	0.85[ASN][1000 genomes]
rs7136561	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7311663	0.94[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7484827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969186	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7976748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7977613	0.81[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	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875687	ENDOU	cis	Thyroid	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48114000-48134400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:48115600-48135000	Weak transcription	Primary T cells from cord blood	blood
3	chr12:48127600-48135800	Enhancers	Fetal Muscle Trunk	muscle
4	chr12:48128200-48135600	Enhancers	Right Atrium	heart
5	chr12:48128400-48135000	Weak transcription	NHEK	skin
6	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:48129200-48134600	Weak transcription	Fetal Brain Female	brain
8	chr12:48129200-48137600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:48129400-48138600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:48129800-48137600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
13	chr12:48130200-48134800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:48130400-48134600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:48130400-48137600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:48130600-48138800	Weak transcription	Fetal Intestine Large	intestine
17	chr12:48130800-48134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:48131000-48134600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
20	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
21	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:48131400-48134400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48131400-48134800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:48131600-48134400	Weak transcription	HSMMtube	muscle
25	chr12:48131600-48134800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:48131600-48134800	Weak transcription	Stomach Mucosa	stomach
27	chr12:48131600-48134800	Weak transcription	HSMM	muscle
28	chr12:48131600-48135000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:48131600-48135000	Weak transcription	Osteobl	bone
30	chr12:48131600-48135200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:48131600-48136400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:48131600-48136600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr12:48131800-48141000	Weak transcription	Gastric	stomach
34	chr12:48132000-48134600	Genic enhancers	Brain Hippocampus Middle	brain
35	chr12:48132000-48136200	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:48132200-48135000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:48132200-48135200	Weak transcription	Pancreas	Pancrea
38	chr12:48132200-48135200	Weak transcription	NHLF	lung
39	chr12:48132200-48136400	Enhancers	Primary B cells from peripheral blood	blood
40	chr12:48132400-48134400	Enhancers	K562	blood
41	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:48132600-48136000	Enhancers	Primary B cells from cord blood	blood
43	chr12:48132600-48136400	Enhancers	Adipose Nuclei	Adipose
44	chr12:48132800-48136600	Enhancers	Primary T cells fromperipheralblood	blood
45	chr12:48133000-48134400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:48133200-48135200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:48133200-48135800	Enhancers	Left Ventricle	heart
48	chr12:48133400-48135600	Enhancers	Lung	lung
49	chr12:48133400-48135800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr12:48133400-48135800	Enhancers	Right Ventricle	heart

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