Variant report

Variant	rs8039651
Chromosome Location	chr15:62359350-62359351
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	chr15:62352114..62355489-chr15:62359291..62363476,4	MCF-7	breast:
2	chr15:62160043..62163025-chr15:62359293..62361455,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129003	Chromatin interaction
ENSG00000259251	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10047986	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1030859	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1030860	0.99[ASN][1000 genomes]
rs1030861	0.99[ASN][1000 genomes]
rs10468026	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519157	0.85[EUR][1000 genomes]
rs10851707	0.99[ASN][1000 genomes]
rs11071642	0.85[CEU][hapmap]
rs11071649	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11629596	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632441	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11633500	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11635977	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11635980	0.86[EUR][1000 genomes]
rs11639482	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12438690	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12438803	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439356	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]
rs12440524	0.86[EUR][1000 genomes]
rs12442212	0.96[CEU][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442675	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12592402	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12593844	0.93[GIH][hapmap];0.82[MEX][hapmap]
rs12594658	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12594946	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12899801	0.93[GIH][hapmap];0.82[MEX][hapmap]
rs12900645	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12900703	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12912208	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12913951	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1344601	0.96[CEU][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs1436958	0.85[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1436961	0.99[ASN][1000 genomes]
rs1436963	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1436964	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1436966	0.81[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1534542	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17205407	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17205463	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17271340	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs17271403	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17271431	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17271438	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1836996	0.97[ASN][1000 genomes]
rs2162062	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs2414753	0.85[CEU][hapmap]
rs2414754	0.82[CEU][hapmap]
rs28542204	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28837073	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2899677	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34096515	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34138933	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35123892	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3784445	0.85[CEU][hapmap]
rs3784633	0.96[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs3784634	0.85[CEU][hapmap]
rs4143841	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4143842	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4143843	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4564516	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774427	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs4775455	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4775457	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775458	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62007368	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62008532	0.86[EUR][1000 genomes]
rs7162536	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172967	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs7177276	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177711	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178424	0.96[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178540	0.96[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178945	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182842	0.88[ASN][1000 genomes]
rs731820	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8025877	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8026008	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027751	0.81[CEU][hapmap]
rs8029942	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8032433	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8033816	0.91[GIH][hapmap];0.85[YRI][hapmap]
rs8034216	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs8034335	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs8038932	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8039105	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs893156	0.96[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs893157	0.85[CEU][hapmap]
rs893158	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs933807	0.96[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs9989353	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv3341159	chr15:62359285-62361833	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv3358286	chr15:62359310-62361608	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8039651	TPM1	cis	cerebellum	SCAN
rs8039651	VPS13C	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62356600-62360000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr15:62357200-62360400	Weak transcription	Hela-S3	cervix
3	chr15:62358400-62359600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr15:62358600-62359400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr15:62358600-62359600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
6	chr15:62358600-62359800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:62358600-62360000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:62358600-62360000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
9	chr15:62358600-62360000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:62358600-62360000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
11	chr15:62358600-62360000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr15:62358600-62360000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:62358600-62360000	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
15	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
17	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr15:62358600-62361000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr15:62358800-62359400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr15:62358800-62359400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr15:62358800-62359400	Bivalent Enhancer	Fetal Brain Male	brain
22	chr15:62358800-62359400	Bivalent/Poised TSS	Fetal Brain Female	brain
23	chr15:62358800-62359400	Bivalent Enhancer	Fetal Lung	lung
24	chr15:62358800-62359400	Flanking Active TSS	Psoas Muscle	Psoas
25	chr15:62358800-62359400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
26	chr15:62358800-62359400	Flanking Active TSS	HUVEC	blood vessel
27	chr15:62358800-62359600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr15:62358800-62359600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:62358800-62359600	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
30	chr15:62358800-62359600	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr15:62358800-62359800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
32	chr15:62358800-62359800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr15:62358800-62359800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr15:62358800-62359800	Active TSS	Stomach Mucosa	stomach
35	chr15:62358800-62359800	Flanking Bivalent TSS/Enh	Osteobl	bone
36	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
37	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
38	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
39	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
40	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
41	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
43	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
44	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
45	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr15:62358800-62360000	Flanking Active TSS	HepG2	liver
47	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	NH-A	brain
48	chr15:62358800-62360200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:62358800-62360200	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr15:62358800-62360800	Active TSS	Esophagus	oesophagus

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