Variant report

Variant	rs1408928
Chromosome Location	chr13:75980470-75980471
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1028793	1.00[ASN][1000 genomes]
rs10507830	1.00[JPT][hapmap]
rs1105687	1.00[ASN][1000 genomes]
rs17064386	1.00[ASN][1000 genomes]
rs17064454	1.00[JPT][hapmap]
rs2025620	0.82[ASN][1000 genomes]
rs2031505	1.00[JPT][hapmap]
rs2031506	1.00[JPT][hapmap]
rs4280128	1.00[ASN][1000 genomes]
rs4340196	1.00[JPT][hapmap]
rs4530013	1.00[ASN][1000 genomes]
rs4883997	0.82[ASN][1000 genomes]
rs4885295	1.00[JPT][hapmap]
rs7321494	0.82[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs7990050	1.00[ASN][1000 genomes]
rs9318344	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9530434	1.00[ASN][1000 genomes]
rs9573539	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498067	chr13:75178898-76012362	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv455987	chr13:75972846-76090084	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv562346	chr13:75972846-76090084	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1408928	KLF12	cis	parietal	SCAN
rs1408928	C13orf34	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:75973400-75987200	Weak transcription	Gastric	stomach
2	chr13:75975200-75981000	Weak transcription	Pancreas	Pancrea
3	chr13:75975600-75980600	Weak transcription	Right Atrium	heart
4	chr13:75976200-75982000	Enhancers	Fetal Heart	heart
5	chr13:75976600-75980800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:75976600-75981000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:75977200-75984400	Weak transcription	Lung	lung
8	chr13:75977400-75980600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:75977400-75984200	Weak transcription	Left Ventricle	heart
10	chr13:75977400-75984200	Weak transcription	GM12878-XiMat	blood
11	chr13:75977400-75990600	Weak transcription	Brain Anterior Caudate	brain
12	chr13:75978000-75982000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr13:75978000-75982400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr13:75978400-75981200	Enhancers	Fetal Kidney	kidney
15	chr13:75978400-75981800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr13:75979000-75981000	Enhancers	Fetal Muscle Leg	muscle
17	chr13:75979600-75981000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:75979800-75980600	Weak transcription	Psoas Muscle	Psoas
19	chr13:75979800-75980600	Enhancers	HSMMtube	muscle
20	chr13:75979800-75980800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr13:75979800-75980800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:75979800-75981400	Enhancers	Adipose Nuclei	Adipose
23	chr13:75979800-75989400	Weak transcription	HSMM	muscle
24	chr13:75980000-75980600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr13:75980000-75980600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr13:75980000-75980800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr13:75980000-75980800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:75980000-75980800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr13:75980000-75980800	Enhancers	Fetal Lung	lung
30	chr13:75980000-75981200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr13:75980000-75981200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr13:75980000-75981200	Enhancers	NHDF-Ad	bronchial
33	chr13:75980000-75981200	Enhancers	Osteobl	bone
34	chr13:75980000-75981400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr13:75980200-75980600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:75980200-75980800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr13:75980200-75980800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:75980200-75980800	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr13:75980200-75980800	Active TSS	Ovary	ovary
40	chr13:75980200-75981400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr13:75980200-75982000	Enhancers	HepG2	liver

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