Variant report

Variant	rs12546843
Chromosome Location	chr8:105508810-105508811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:105494376-105512670	K562	blood:	n/a	n/a

Variant related genes	Relation type
LRP12	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11987427	0.85[JPT][hapmap]
rs12543329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12543736	0.87[ASN][1000 genomes]
rs12544422	0.87[ASN][1000 genomes]
rs12550349	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12674790	0.85[JPT][hapmap]
rs12680920	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12681417	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs2298840	0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs3750187	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4461873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4474003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4602859	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4609171	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62510142	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66479713	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67341229	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67403507	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6988526	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72679139	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72679149	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73295140	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7813115	0.85[JPT][hapmap]
rs7814352	0.85[JPT][hapmap]
rs7845549	0.85[JPT][hapmap]

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	nsv1016087	chr8:105228670-105934368	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1026754	chr8:105382508-106030916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv539709	chr8:105382508-106030916	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv831417	chr8:105455814-105625608	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12546843	DPYS	cis	cerebellum	SCAN
rs12546843	LRP12	cis	cerebellum	SCAN
rs12546843	LRP12	cis	parietal	SCAN
rs12546843	LRP12	cis	Skin Sun Exposed Lower leg	GTEx
rs12546843	DCAF13	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:105489400-105512800	Weak transcription	Gastric	stomach
2	chr8:105491400-105510000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr8:105491400-105517200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr8:105495600-105509200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr8:105495600-105525800	Weak transcription	Psoas Muscle	Psoas
6	chr8:105499200-105542200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr8:105500800-105519800	Strong transcription	Dnd41	blood
8	chr8:105501000-105509200	Weak transcription	Lung	lung
9	chr8:105501200-105509000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:105501400-105509200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr8:105501400-105509400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr8:105501400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:105501400-105515000	Weak transcription	Spleen	Spleen
14	chr8:105501400-105516200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr8:105501400-105517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr8:105501400-105517400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr8:105501600-105509200	Weak transcription	Brain Substantia Nigra	brain
18	chr8:105501600-105509200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr8:105501600-105509400	Weak transcription	HMEC	breast
20	chr8:105501600-105512200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr8:105501600-105520800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr8:105501800-105509200	Weak transcription	NHLF	lung
23	chr8:105501800-105518800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr8:105501800-105521000	Weak transcription	NHEK	skin
25	chr8:105502000-105510800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:105502000-105518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr8:105502200-105509400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr8:105503200-105511200	Weak transcription	Esophagus	oesophagus
29	chr8:105503400-105509400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr8:105503400-105509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr8:105503600-105509000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr8:105503600-105509000	Weak transcription	HSMM	muscle
33	chr8:105503600-105509200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:105503600-105509200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr8:105503600-105509200	Weak transcription	Primary T cells from cord blood	blood
36	chr8:105503600-105509200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr8:105503600-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr8:105503600-105509200	Weak transcription	Adipose Nuclei	Adipose
39	chr8:105503600-105509200	Weak transcription	Fetal Brain Male	brain
40	chr8:105503600-105509200	Weak transcription	Fetal Intestine Large	intestine
41	chr8:105503600-105509200	Weak transcription	Fetal Kidney	kidney
42	chr8:105503600-105509200	Weak transcription	Fetal Lung	lung
43	chr8:105503600-105509200	Weak transcription	Ovary	ovary
44	chr8:105503600-105509400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr8:105503600-105509600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr8:105503600-105519000	Weak transcription	Fetal Intestine Small	intestine
47	chr8:105503600-105520800	Weak transcription	Pancreas	Pancrea
48	chr8:105503600-105525800	Weak transcription	HUVEC	blood vessel
49	chr8:105503800-105509200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr8:105503800-105509200	Weak transcription	Fetal Muscle Leg	muscle

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