Variant report

Variant	rs10441557
Chromosome Location	chr8:48309587-48309588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10099236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10108778	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10957370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11776864	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12547497	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13279327	0.87[CHD][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap]
rs2362555	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34506397	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35332377	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4594029	0.86[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.86[YRI][hapmap]
rs4873088	0.83[AMR][1000 genomes]
rs4873101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4873463	0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs58299877	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6472452	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6473996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6981485	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6987882	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6990363	0.81[EUR][1000 genomes]
rs7825148	0.97[EUR][1000 genomes]
rs7828350	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7832841	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7833589	0.86[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs7846620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015347	chr8:47698082-48318579	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv539593	chr8:47698082-48318579	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv2758155	chr8:48188989-48321308	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2759610	chr8:48188989-48321308	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv1817304	chr8:48205314-48321308	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1034660	chr8:48265109-48411279	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1018457	chr8:48289643-48321308	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
10	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10441557	KIAA0146	cis	parietal	SCAN
rs10441557	MCM4	cis	lymphoblastoid	seeQTL
rs10441557	SNAI2	cis	cerebellum	SCAN
rs10441557	MCM4	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48248800-48309600	Weak transcription	Thymus	Thymus
2	chr8:48262400-48309600	Weak transcription	Fetal Stomach	stomach
3	chr8:48279000-48310200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr8:48280600-48311200	Weak transcription	Aorta	Aorta
5	chr8:48282200-48311200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr8:48282200-48312200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr8:48282400-48321200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr8:48290400-48311400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr8:48290800-48322200	Weak transcription	Liver	Liver
10	chr8:48290800-48347400	Weak transcription	HepG2	liver
11	chr8:48291400-48310000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr8:48291800-48309600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr8:48292000-48310800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr8:48293000-48312600	Weak transcription	Fetal Thymus	thymus
15	chr8:48293200-48315000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr8:48294400-48309600	Weak transcription	Fetal Intestine Small	intestine
17	chr8:48295800-48311200	Weak transcription	Lung	lung
18	chr8:48295800-48324400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr8:48296800-48309600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr8:48297400-48310600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr8:48297400-48312400	Weak transcription	Left Ventricle	heart
22	chr8:48297600-48309800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:48298200-48310200	Weak transcription	A549	lung
24	chr8:48298200-48310400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:48298200-48325600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr8:48298400-48309600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr8:48298400-48310800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:48298400-48316400	Weak transcription	NHLF	lung
29	chr8:48298400-48325400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr8:48298600-48325600	Weak transcription	Osteobl	bone
31	chr8:48299600-48331600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr8:48300000-48309600	Weak transcription	Spleen	Spleen
33	chr8:48300000-48311400	Weak transcription	Esophagus	oesophagus
34	chr8:48300000-48312200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr8:48300000-48318600	Weak transcription	Stomach Mucosa	stomach
36	chr8:48300200-48309600	Weak transcription	Gastric	stomach
37	chr8:48300200-48310200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:48300200-48310800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr8:48300200-48311200	Weak transcription	Pancreas	Pancrea
40	chr8:48300200-48311400	Weak transcription	Hela-S3	cervix
41	chr8:48300400-48309600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr8:48300400-48331400	Weak transcription	Fetal Brain Male	brain
43	chr8:48300600-48320200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:48300800-48325600	Weak transcription	HMEC	breast
45	chr8:48301400-48341200	Weak transcription	HSMMtube	muscle
46	chr8:48301600-48310000	Weak transcription	Primary B cells from cord blood	blood
47	chr8:48301600-48310200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr8:48301600-48310400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr8:48301600-48311200	Weak transcription	K562	blood
50	chr8:48301600-48325600	Weak transcription	Adipose Nuclei	Adipose

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