Variant report

Variant	rs10450961
Chromosome Location	chr15:57130517-57130518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57126017..57127924-chr15:57129795..57132351,2	K562	blood:
2	chr15:57115805..57118368-chr15:57128099..57130760,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MNS1-10	chr15:57130516-57130873	NONHSAT044032

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1012321	0.87[EUR][1000 genomes]
rs10518878	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11855646	0.84[EUR][1000 genomes]
rs11858368	0.85[EUR][1000 genomes]
rs13379960	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1430819	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1441235	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1441236	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1612205	0.81[EUR][1000 genomes]
rs1647392	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1657930	0.80[EUR][1000 genomes]
rs1657934	0.82[EUR][1000 genomes]
rs1657935	0.83[EUR][1000 genomes]
rs1657936	0.83[EUR][1000 genomes]
rs1657937	0.83[EUR][1000 genomes]
rs1657938	0.81[EUR][1000 genomes]
rs1660948	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1660951	0.82[EUR][1000 genomes]
rs1660961	0.88[EUR][1000 genomes]
rs1967352	0.89[EUR][1000 genomes]
rs1967353	0.87[EUR][1000 genomes]
rs2161933	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2163369	0.90[EUR][1000 genomes]
rs2414487	0.84[EUR][1000 genomes]
rs28371400	0.84[EUR][1000 genomes]
rs28468978	0.86[EUR][1000 genomes]
rs28568712	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28609621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28736360	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28874022	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4313751	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56965085	0.87[EUR][1000 genomes]
rs6493892	0.84[AMR][1000 genomes]
rs6493893	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493894	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67114210	0.92[EUR][1000 genomes]
rs67278720	0.81[EUR][1000 genomes]
rs67622899	0.87[EUR][1000 genomes]
rs68083905	0.92[EUR][1000 genomes]
rs7163302	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7166876	0.85[AMR][1000 genomes]
rs7182691	0.85[AMR][1000 genomes]
rs72747165	0.86[EUR][1000 genomes]
rs7359253	0.82[EUR][1000 genomes]
rs8026149	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8040866	0.90[EUR][1000 genomes]
rs8042606	0.87[EUR][1000 genomes]
rs9919955	0.85[AMR][1000 genomes];0.82[EUR][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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10450961	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57110000-57138600	Weak transcription	Left Ventricle	heart
2	chr15:57124000-57130600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr15:57124800-57131800	Weak transcription	HMEC	breast
4	chr15:57125400-57140400	Weak transcription	Brain Angular Gyrus	brain
5	chr15:57125400-57141000	Weak transcription	Fetal Lung	lung
6	chr15:57125400-57141000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:57128000-57131000	Enhancers	Adipose Nuclei	Adipose
8	chr15:57128200-57140400	Weak transcription	Brain Anterior Caudate	brain
9	chr15:57128200-57158600	Weak transcription	Ovary	ovary
10	chr15:57128400-57140000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:57128400-57140400	Weak transcription	Right Ventricle	heart
12	chr15:57128600-57131800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:57129000-57131200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:57129000-57132000	Enhancers	Dnd41	blood
15	chr15:57129000-57132200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:57129200-57131800	Enhancers	Primary B cells from peripheral blood	blood
17	chr15:57129400-57130600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:57129400-57137400	Weak transcription	Fetal Kidney	kidney
19	chr15:57129400-57142600	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:57129800-57133000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:57130000-57130600	Weak transcription	NHDF-Ad	bronchial
22	chr15:57130000-57130800	Weak transcription	Osteobl	bone
23	chr15:57130000-57131000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:57130000-57131800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:57130000-57131800	Enhancers	GM12878-XiMat	blood
26	chr15:57130200-57130600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:57130200-57130800	Enhancers	Fetal Thymus	thymus
28	chr15:57130200-57131200	Weak transcription	Primary B cells from cord blood	blood
29	chr15:57130400-57131000	Enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links