Variant report

Variant	rs4474003
Chromosome Location	chr8:105504722-105504723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:105504212..105505135-chr8:105771631..105772165,4	K562	blood:
2	chr8:105454151..105454949-chr8:105504221..105505138,2	MCF-7	breast:
3	chr8:105337371..105338281-chr8:105504200..105504994,3	K562	blood:
4	chr8:104776641..104777197-chr8:105504360..105505105,2	MCF-7	breast:
5	chr8:105499986..105502315-chr8:105504573..105506313,2	MCF-7	breast:
6	chr8:104776370..104777203-chr8:105504141..105505133,3	K562	blood:
7	chr8:104776210..104777349-chr8:105503586..105504992,8	MCF-7	breast:
8	chr8:104808701..104809570-chr8:105504240..105505101,3	MCF-7	breast:
9	chr8:105487780..105488639-chr8:105504399..105505102,3	MCF-7	breast:
10	chr8:105337513..105338290-chr8:105504452..105505411,2	MCF-7	breast:

No data

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11987427	0.86[JPT][hapmap]
rs12543329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[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]
rs12546843	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]
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	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2298840	0.89[CHB][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs3750187	0.94[CEU][hapmap];0.94[CHB][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4461873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
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	0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4474003	LRP12	cis	Skin Sun Exposed Lower leg	GTEx
rs4474003	LRP12	cis	lesional skin	skin_eQTL

Chromatin state (count:95 , 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	chr8:105492200-105505800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr8:105495400-105507200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:105495600-105509200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr8:105495600-105525800	Weak transcription	Psoas Muscle	Psoas
8	chr8:105499200-105542200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:105500800-105519800	Strong transcription	Dnd41	blood
10	chr8:105501000-105509200	Weak transcription	Lung	lung
11	chr8:105501200-105509000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:105501400-105504800	Weak transcription	Brain Hippocampus Middle	brain
13	chr8:105501400-105505800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr8:105501400-105509200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr8:105501400-105509400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr8:105501400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr8:105501400-105515000	Weak transcription	Spleen	Spleen
18	chr8:105501400-105516200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr8:105501400-105517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr8:105501400-105517400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr8:105501600-105504800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:105501600-105509200	Weak transcription	Brain Substantia Nigra	brain
23	chr8:105501600-105509200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr8:105501600-105509400	Weak transcription	HMEC	breast
25	chr8:105501600-105512200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr8:105501600-105520800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr8:105501800-105505600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr8:105501800-105509200	Weak transcription	NHLF	lung
29	chr8:105501800-105518800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr8:105501800-105521000	Weak transcription	NHEK	skin
31	chr8:105502000-105510800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:105502000-105518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr8:105502200-105509400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr8:105502800-105505200	Strong transcription	Osteobl	bone
35	chr8:105503000-105505400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr8:105503200-105511200	Weak transcription	Esophagus	oesophagus
37	chr8:105503400-105504800	Weak transcription	Brain Anterior Caudate	brain
38	chr8:105503400-105505800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr8:105503400-105505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr8:105503400-105509400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr8:105503400-105509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr8:105503600-105504800	Weak transcription	K562	blood
43	chr8:105503600-105505200	Weak transcription	Fetal Heart	heart
44	chr8:105503600-105505600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr8:105503600-105505600	Weak transcription	Thymus	Thymus
46	chr8:105503600-105505800	Weak transcription	Brain Germinal Matrix	brain
47	chr8:105503600-105506000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:105503600-105509000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr8:105503600-105509000	Weak transcription	HSMM	muscle
50	chr8:105503600-105509200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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