Variant report

Variant	rs12439356
Chromosome Location	chr15:62380595-62380596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:62363137..62365587-chr15:62379129..62382052,2	MCF-7	breast:
2	chr15:62372730..62374756-chr15:62378857..62380874,2	MCF-7	breast:
3	chr15:62367214..62369987-chr15:62379884..62381677,2	MCF-7	breast:
4	chr15:62364024..62367163-chr15:62377936..62381314,4	MCF-7	breast:
5	chr15:62358958..62360819-chr15:62378474..62381004,3	MCF-7	breast:
6	chr15:62379222..62381891-chr15:62428344..62430839,2	MCF-7	breast:
7	chr15:62378815..62381663-chr15:62419269..62421288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198535	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10047986	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1030859	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1030860	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1030861	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10468026	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10519157	0.87[EUR][1000 genomes]
rs10851707	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11071642	0.81[CEU][hapmap]
rs11071649	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11629596	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11632441	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11633500	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11635977	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11635980	0.85[EUR][1000 genomes]
rs11639482	0.93[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12438690	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438803	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12440524	0.85[EUR][1000 genomes]
rs12442212	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442675	0.96[CEU][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12592402	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12593844	0.83[MEX][hapmap]
rs12594658	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12594946	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12899801	0.83[MEX][hapmap]
rs12900645	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12900703	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12912208	0.85[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12913951	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1344601	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1436958	0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1436961	0.87[ASN][1000 genomes]
rs1436963	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1436964	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1436966	0.85[CEU][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1534542	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs17205407	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17205463	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17271340	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs17271403	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17271431	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17271438	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1836996	0.86[ASN][1000 genomes]
rs2162062	0.93[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2414753	0.81[CEU][hapmap]
rs28542204	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28837073	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2899677	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34096515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34138933	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35123892	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3784445	0.82[CEU][hapmap]
rs3784633	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs3784634	0.81[CEU][hapmap]
rs4143841	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4143842	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4143843	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4564516	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774427	0.81[CEU][hapmap]
rs4775455	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4775457	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775458	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007368	0.84[AMR][1000 genomes]
rs62008532	0.84[EUR][1000 genomes]
rs7162536	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7172967	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs7177276	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7177711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178424	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178540	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182842	0.97[ASN][1000 genomes]
rs731820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8025877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026008	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8029942	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8032433	0.88[CEU][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8034216	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs8034335	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs8038932	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8039105	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs8039651	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs893156	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs893157	0.89[CEU][hapmap]
rs893158	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs933807	0.93[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs9989353	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv948606	chr15:62364932-63088916	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12439356	VPS13C	cis	cerebellum	SCAN
rs12439356	TPM1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62379200-62382000	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr15:62379600-62380600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:62379600-62380600	Enhancers	Hela-S3	cervix
4	chr15:62379600-62380800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:62379600-62381000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr15:62379600-62381000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr15:62379600-62381200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:62379800-62380600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:62379800-62380600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:62379800-62380600	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:62379800-62380600	Enhancers	Fetal Muscle Leg	muscle
12	chr15:62379800-62380600	Enhancers	Pancreas	Pancrea
13	chr15:62379800-62380600	Enhancers	Dnd41	blood
14	chr15:62379800-62380600	Enhancers	NHDF-Ad	bronchial
15	chr15:62379800-62380800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:62379800-62381200	Enhancers	Right Atrium	heart
17	chr15:62379800-62382000	Enhancers	HUVEC	blood vessel
18	chr15:62380000-62380600	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr15:62380000-62380800	Enhancers	Adipose Nuclei	Adipose
20	chr15:62380200-62380600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:62380200-62380600	Enhancers	Liver	Liver
22	chr15:62380200-62380600	Enhancers	Fetal Lung	lung
23	chr15:62380200-62381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:62380200-62381800	Weak transcription	NHEK	skin
25	chr15:62380400-62380600	Enhancers	Small Intestine	intestine
26	chr15:62380400-62380800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:62380400-62381000	Enhancers	Rectal Mucosa Donor 31	rectum

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