Variant report

Variant	rs10518876
Chromosome Location	chr15:57065787-57065788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57061117..57063691-chr15:57064747..57067595,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1010699	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11071282	0.93[MEX][hapmap]
rs11071283	0.93[MEX][hapmap]
rs11071294	0.86[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11630334	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11634444	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11636534	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12324492	0.81[ASN][1000 genomes]
rs1627133	0.84[ASN][1000 genomes]
rs1647381	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1657928	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1657932	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1657933	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1657941	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1657942	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1660965	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1660966	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1680488	1.00[MEX][hapmap]
rs16977060	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16977067	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16977078	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2113678	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2113679	0.85[ASN][1000 genomes]
rs2165460	0.84[ASN][1000 genomes]
rs2247641	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28463927	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28678122	0.93[MEX][hapmap]
rs4774891	0.82[GIH][hapmap]
rs534005	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs56107629	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7164084	0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175576	0.83[ASN][1000 genomes]
rs7182346	0.86[GIH][hapmap];1.00[MEX][hapmap]
rs809459	0.86[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10518876	TCF12	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57056800-57066400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr15:57058000-57066400	Weak transcription	Thymus	Thymus
3	chr15:57063400-57068000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr15:57064800-57065800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr15:57064800-57065800	Weak transcription	HUVEC	blood vessel
6	chr15:57064800-57066000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:57064800-57066000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:57064800-57066000	Enhancers	Fetal Lung	lung
9	chr15:57064800-57066000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr15:57065000-57065800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr15:57065000-57065800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr15:57065000-57065800	Enhancers	Fetal Kidney	kidney
13	chr15:57065000-57065800	Enhancers	Stomach Mucosa	stomach
14	chr15:57065000-57065800	Flanking Active TSS	HepG2	liver
15	chr15:57065000-57066000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr15:57065000-57066000	Enhancers	Adipose Nuclei	Adipose
17	chr15:57065000-57066000	Enhancers	Fetal Stomach	stomach
18	chr15:57065000-57066000	Enhancers	HSMM	muscle
19	chr15:57065000-57066000	Enhancers	NHLF	lung
20	chr15:57065000-57066200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:57065200-57065800	Enhancers	Aorta	Aorta
22	chr15:57065200-57066000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:57065200-57066000	Flanking Active TSS	Liver	Liver
24	chr15:57065200-57066000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr15:57065200-57066000	Enhancers	Ovary	ovary
26	chr15:57065200-57066000	Enhancers	Psoas Muscle	Psoas
27	chr15:57065200-57066000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr15:57065200-57066000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr15:57065200-57066000	Enhancers	K562	blood
30	chr15:57065200-57066000	Enhancers	NH-A	brain
31	chr15:57065200-57068400	Enhancers	Fetal Thymus	thymus
32	chr15:57065200-57069000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:57065400-57065800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr15:57065400-57065800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:57065400-57065800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr15:57065400-57065800	Flanking Active TSS	HSMMtube	muscle
37	chr15:57065400-57066200	Enhancers	A549	lung
38	chr15:57065400-57066400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr15:57065600-57065800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
40	chr15:57065600-57065800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr15:57065600-57065800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:57065600-57065800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:57065600-57065800	Enhancers	NHEK	skin
44	chr15:57065600-57066000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
45	chr15:57065600-57066000	Enhancers	Fetal Muscle Leg	muscle
46	chr15:57065600-57066000	Enhancers	Stomach Smooth Muscle	stomach
47	chr15:57065600-57066200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr15:57065600-57066200	Enhancers	Osteobl	bone
49	chr15:57065600-57067800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:57065600-57068800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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