Variant report

Variant	rs12405017
Chromosome Location	chr1:86018543-86018544
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	chr1:86014905..86019706-chr1:86042363..86049373,11	MCF-7	breast:
2	chr1:86017811..86020709-chr1:86023233..86025891,2	K562	blood:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11161652	1.00[YRI][hapmap]
rs12067136	1.00[YRI][hapmap]
rs12133722	1.00[YRI][hapmap]
rs12140935	1.00[YRI][hapmap]
rs12405846	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12410234	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2026774	0.87[CHD][hapmap]
rs2970548	0.85[CHD][hapmap]
rs4949917	0.87[CHD][hapmap]
rs4949918	0.87[CHD][hapmap]
rs6694808	0.87[CHD][hapmap]
rs7533395	0.87[CHD][hapmap]
rs821400	0.87[CHD][hapmap]
rs9793556	0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86010800-86020200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:86011000-86018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:86011000-86019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:86011000-86019200	Weak transcription	Left Ventricle	heart
5	chr1:86011600-86019600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:86011600-86020800	Weak transcription	Hela-S3	cervix
7	chr1:86011600-86035200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:86011800-86019600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:86012200-86019400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:86014200-86019400	Weak transcription	Fetal Heart	heart
11	chr1:86015200-86020400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:86015400-86019600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:86015400-86019600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:86015400-86019600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:86015400-86020200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:86015600-86020400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:86016000-86022200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:86016200-86022400	Enhancers	Rectal Smooth Muscle	rectum
19	chr1:86016400-86019800	Enhancers	Aorta	Aorta
20	chr1:86016800-86020400	Weak transcription	Brain Anterior Caudate	brain
21	chr1:86016800-86022200	Enhancers	Colon Smooth Muscle	Colon
22	chr1:86017000-86019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:86017000-86019200	Weak transcription	HMEC	breast
24	chr1:86017000-86019200	Weak transcription	NHEK	skin
25	chr1:86017200-86019200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:86017200-86019600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:86017200-86020000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:86017200-86032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:86017400-86019000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:86017400-86019200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:86017400-86019200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:86017400-86019600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:86017400-86019600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:86017400-86020400	Weak transcription	A549	lung
35	chr1:86017400-86020400	Weak transcription	HSMMtube	muscle
36	chr1:86017400-86022200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:86017600-86018600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:86017600-86018600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:86017600-86018600	Weak transcription	NHDF-Ad	bronchial
40	chr1:86017600-86018800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:86017600-86018800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:86017600-86019600	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr1:86017600-86020400	Weak transcription	Fetal Lung	lung
44	chr1:86017600-86020600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:86017600-86020600	Weak transcription	HUVEC	blood vessel
46	chr1:86017600-86023800	Genic enhancers	Osteobl	bone
47	chr1:86017800-86018600	Weak transcription	HSMM	muscle
48	chr1:86017800-86019200	Weak transcription	Lung	lung
49	chr1:86018000-86019200	Weak transcription	NHLF	lung
50	chr1:86018200-86019000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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