Variant report

Variant	rs12256403
Chromosome Location	chr10:28569959-28569960
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	MAFK	chr10:28569644-28569962	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
MPP7	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10763654	0.82[CHB][hapmap]
rs10763655	0.86[CHB][hapmap]
rs10826435	0.82[CHB][hapmap]
rs10826444	0.82[ASN][1000 genomes]
rs10826449	0.82[CHB][hapmap]
rs11006957	0.82[CHB][hapmap]
rs11006965	0.82[CHB][hapmap]
rs1144514	0.82[EUR][1000 genomes]
rs1148173	0.94[ASN][1000 genomes]
rs1148174	0.86[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1148175	0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs12248351	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1249420	0.82[EUR][1000 genomes]
rs1413905	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs1418759	0.82[CHB][hapmap]
rs1870097	0.82[CHB][hapmap]
rs2124955	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2607540	0.82[CHB][hapmap]
rs3847388	0.82[CHB][hapmap]
rs6481515	0.82[CHB][hapmap]
rs7088465	0.82[CHB][hapmap]
rs7905490	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7913970	0.82[CHB][hapmap]
rs7918097	0.82[ASN][1000 genomes]
rs9663446	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1040916	chr10:28558982-28579141	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
6	nsv466856	chr10:28562647-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv470929	chr10:28562647-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv550285	chr10:28562647-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv818752	chr10:28562647-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv437663	chr10:28562647-28585496	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
11	esv2760125	chr10:28563995-28570599	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1036270	chr10:28563995-28574327	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1045247	chr10:28563995-28574624	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1039546	chr10:28563995-28579141	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
15	esv2421445	chr10:28564207-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv3693051	chr10:28564732-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv818753	chr10:28564732-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv515548	chr10:28564732-28579969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
19	esv12765	chr10:28564737-28573369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv438167	chr10:28567807-28569959	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv818754	chr10:28567807-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12256403	C8orf41	trans	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28550400-28582600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr10:28553000-28570800	Weak transcription	Esophagus	oesophagus
3	chr10:28556200-28570800	Weak transcription	Primary B cells from cord blood	blood
4	chr10:28556400-28571000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:28559600-28570800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr10:28562600-28570800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:28564000-28573200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:28564200-28573200	Weak transcription	Primary T cells from cord blood	blood
9	chr10:28564400-28570800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr10:28564800-28570800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr10:28564800-28572800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:28564800-28573000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr10:28565000-28571000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr10:28566200-28571000	Weak transcription	HepG2	liver
15	chr10:28566800-28573000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr10:28567800-28570200	Enhancers	Fetal Heart	heart
17	chr10:28568200-28570800	Weak transcription	Fetal Muscle Leg	muscle
18	chr10:28568400-28570600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr10:28568400-28570800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:28568400-28570800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr10:28568400-28573200	Weak transcription	Right Ventricle	heart
22	chr10:28568800-28570400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr10:28568800-28570800	Enhancers	Osteobl	bone
24	chr10:28568800-28571200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr10:28568800-28571200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:28568800-28571400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr10:28569000-28571800	Enhancers	Stomach Smooth Muscle	stomach
28	chr10:28569000-28578400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr10:28569200-28570000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr10:28569200-28570800	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr10:28569400-28570200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:28569400-28570400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr10:28569400-28570600	Enhancers	NH-A	brain
34	chr10:28569400-28572400	Enhancers	Colon Smooth Muscle	Colon
35	chr10:28569600-28570200	Enhancers	HSMMtube	muscle
36	chr10:28569600-28570800	Weak transcription	Lung	lung
37	chr10:28569600-28571800	Enhancers	Pancreas	Pancrea
38	chr10:28569600-28572000	Enhancers	Aorta	Aorta
39	chr10:28569800-28570000	Enhancers	Fetal Kidney	kidney
40	chr10:28569800-28570800	Weak transcription	Left Ventricle	heart
41	chr10:28569800-28570800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr10:28569800-28570800	Weak transcription	HSMM	muscle
43	chr10:28569800-28571000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:28569800-28571000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr10:28569800-28571000	Weak transcription	Psoas Muscle	Psoas

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