Variant report

Variant	rs2161933
Chromosome Location	chr15:57125769-57125770
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	chr15:57118084..57120874-chr15:57123511..57126088,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1012321	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10450961	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10518878	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10851612	0.82[CEU][hapmap]
rs1115019	0.94[CEU][hapmap]
rs11855646	0.86[EUR][1000 genomes]
rs11858368	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13379960	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1430819	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1441235	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1441236	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1612205	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1647378	0.88[ASN][1000 genomes]
rs1647392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1657922	0.94[CEU][hapmap]
rs1657930	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1657934	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1657935	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1657936	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1657937	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1657938	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1657939	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1660948	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1660950	0.92[ASN][1000 genomes]
rs1660951	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1660961	0.89[EUR][1000 genomes]
rs1967352	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1967353	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2163369	0.93[EUR][1000 genomes]
rs2278613	0.88[CEU][hapmap]
rs2414487	0.85[EUR][1000 genomes]
rs28371400	0.85[EUR][1000 genomes]
rs28468978	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28568712	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28609621	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28736360	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28874022	0.94[EUR][1000 genomes]
rs4313751	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774893	0.91[ASN][1000 genomes]
rs4774895	0.91[ASN][1000 genomes]
rs56965085	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493886	0.82[CEU][hapmap]
rs6493893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493894	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67114210	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67278720	0.85[EUR][1000 genomes]
rs67622899	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68083905	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163302	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166876	0.80[EUR][1000 genomes]
rs7175191	0.94[CEU][hapmap]
rs7178196	0.90[AMR][1000 genomes]
rs72747165	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7359253	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8026149	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8040866	0.93[EUR][1000 genomes]
rs8042606	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9919955	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
rs2161933	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57110000-57138600	Weak transcription	Left Ventricle	heart
2	chr15:57113000-57130400	Weak transcription	Thymus	Thymus
3	chr15:57117000-57129000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:57122600-57128000	Weak transcription	Brain Germinal Matrix	brain
5	chr15:57123200-57125800	Enhancers	Brain Cingulate Gyrus	brain
6	chr15:57124000-57130600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:57124600-57128000	Weak transcription	Fetal Thymus	thymus
8	chr15:57124800-57126200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr15:57124800-57127600	Weak transcription	Fetal Heart	heart
10	chr15:57124800-57127800	Weak transcription	Ovary	ovary
11	chr15:57124800-57128000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:57124800-57128000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:57124800-57129000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:57124800-57129400	Weak transcription	NHDF-Ad	bronchial
15	chr15:57124800-57131800	Weak transcription	HMEC	breast
16	chr15:57125000-57125800	Enhancers	Stomach Smooth Muscle	stomach
17	chr15:57125000-57129000	Weak transcription	NH-A	brain
18	chr15:57125000-57129000	Weak transcription	Osteobl	bone
19	chr15:57125200-57127400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:57125200-57127600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:57125200-57127600	Weak transcription	Brain Substantia Nigra	brain
22	chr15:57125200-57127800	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:57125200-57128000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:57125200-57128000	Weak transcription	Fetal Muscle Leg	muscle
25	chr15:57125200-57129000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:57125400-57127200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:57125400-57127400	Weak transcription	Brain Anterior Caudate	brain
28	chr15:57125400-57127600	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:57125400-57127800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:57125400-57128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:57125400-57129000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:57125400-57140400	Weak transcription	Brain Angular Gyrus	brain
33	chr15:57125400-57141000	Weak transcription	Fetal Lung	lung
34	chr15:57125400-57141000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:57125600-57126000	Weak transcription	Adipose Nuclei	Adipose

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