Variant report

Variant	rs10441581
Chromosome Location	chr8:48545961-48545962
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	chr8:48544030..48546745-chr8:48645753..48648082,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10094128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10109113	0.80[EUR][1000 genomes]
rs10957370	0.93[JPT][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.91[YRI][hapmap]
rs12674784	0.87[JPT][hapmap]
rs13279327	0.86[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[YRI][hapmap]
rs1542721	0.87[JPT][hapmap]
rs16930163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16930230	0.87[JPT][hapmap]
rs2029239	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2130411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4436571	0.84[EUR][1000 genomes]
rs4486659	0.83[EUR][1000 genomes]
rs4594029	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4873386	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4873446	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4873463	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4873478	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873546	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6472450	0.85[YRI][hapmap]
rs6472452	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs6986054	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7462209	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7827571	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7830859	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7833589	0.87[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap]
rs7842068	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv470211	chr8:48405007-48545961	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1027043	chr8:48444306-48637900	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv539596	chr8:48444306-48637900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10441581	KIAA0146	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48512200-48556600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr8:48519400-48573600	Weak transcription	Primary T cells from cord blood	blood
3	chr8:48523800-48572200	Weak transcription	Primary B cells from cord blood	blood
4	chr8:48525800-48556200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr8:48535200-48547200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:48535600-48554200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr8:48535800-48554000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr8:48540600-48556600	Weak transcription	Right Ventricle	heart
9	chr8:48540800-48556000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr8:48541000-48550200	Weak transcription	Fetal Heart	heart
11	chr8:48541000-48554400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr8:48541200-48556400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr8:48541600-48556600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr8:48542800-48546600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr8:48542800-48546600	Enhancers	Fetal Muscle Leg	muscle
16	chr8:48542800-48546600	Enhancers	Placenta	Placenta
17	chr8:48543000-48546600	Enhancers	Adipose Nuclei	Adipose
18	chr8:48543200-48546200	Enhancers	Brain Hippocampus Middle	brain
19	chr8:48543200-48546400	Enhancers	Brain Substantia Nigra	brain
20	chr8:48543200-48546400	Enhancers	HSMM	muscle
21	chr8:48543200-48546600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:48543400-48546000	Enhancers	Brain Angular Gyrus	brain
23	chr8:48543600-48546000	Enhancers	Stomach Smooth Muscle	stomach
24	chr8:48543600-48546000	Enhancers	NHDF-Ad	bronchial
25	chr8:48543600-48546400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr8:48543600-48546600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr8:48543600-48546800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr8:48543600-48556000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:48543800-48546000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr8:48543800-48546000	Weak transcription	Pancreas	Pancrea
31	chr8:48543800-48548000	Weak transcription	Colonic Mucosa	Colon
32	chr8:48543800-48554200	Weak transcription	Aorta	Aorta
33	chr8:48543800-48556600	Weak transcription	Liver	Liver
34	chr8:48543800-48556600	Weak transcription	Gastric	stomach
35	chr8:48543800-48559400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr8:48544000-48554200	Weak transcription	Fetal Intestine Large	intestine
37	chr8:48544200-48546000	Enhancers	Colon Smooth Muscle	Colon
38	chr8:48544200-48546000	Enhancers	NHLF	lung
39	chr8:48544400-48546800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr8:48544400-48547400	Enhancers	Brain Anterior Caudate	brain
41	chr8:48544600-48546400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr8:48544800-48546000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr8:48544800-48546400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr8:48544800-48546800	Enhancers	Ovary	ovary
45	chr8:48544800-48546800	Enhancers	Right Atrium	heart
46	chr8:48544800-48547400	Enhancers	Psoas Muscle	Psoas
47	chr8:48545000-48547800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr8:48545200-48547400	Enhancers	Fetal Muscle Trunk	muscle
49	chr8:48545400-48546000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr8:48545400-48546000	Enhancers	Rectal Mucosa Donor 29	rectum

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