Variant report

Variant	rs2278812
Chromosome Location	chr17:60040329-60040330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60005078..60007617-chr17:60038546..60041416,2	MCF-7	breast:
2	chr17:60039140..60041434-chr17:60052103..60054723,2	MCF-7	breast:
3	chr17:60040110..60042878-chr17:60047051..60049770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10512492	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs11079459	0.81[EUR][1000 genomes]
rs12450560	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap]
rs12451910	0.83[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs12452094	0.82[JPT][hapmap]
rs12452742	0.82[JPT][hapmap]
rs12600620	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12600909	0.82[JPT][hapmap]
rs12604037	0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap]
rs16945692	0.88[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap]
rs16945753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16945756	0.85[ASN][1000 genomes]
rs16945759	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[ASN][1000 genomes]
rs16945801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2271576	0.88[GIH][hapmap]
rs2378908	0.87[GIH][hapmap];0.85[MEX][hapmap]
rs28431006	0.87[ASW][hapmap]
rs28654524	0.81[ASN][1000 genomes]
rs3744434	0.88[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs3809753	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs3826419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4422036	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs4968408	0.88[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs4968451	0.88[GIH][hapmap];0.93[MEX][hapmap]
rs4968455	0.82[JPT][hapmap]
rs4968456	0.82[JPT][hapmap]
rs4968457	0.81[JPT][hapmap]
rs4968460	0.88[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs4968461	0.86[JPT][hapmap]
rs4968462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4968463	0.88[ASN][1000 genomes]
rs4968464	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4968468	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs57137451	0.84[ASN][1000 genomes]
rs57746689	0.86[ASN][1000 genomes]
rs58241345	0.84[ASN][1000 genomes]
rs58335059	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60053512	0.86[ASN][1000 genomes]
rs6504084	0.81[MEX][hapmap]
rs7212824	0.87[ASW][hapmap]
rs7218724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[ASN][1000 genomes]
rs7221089	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.86[ASN][1000 genomes]
rs8065778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8066964	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8068267	0.81[ASW][hapmap]
rs8074890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8080599	0.88[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs8081917	0.88[GIH][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap]
rs9630736	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9899780	0.80[ASW][hapmap]
rs9909145	0.87[ASW][hapmap]
rs9913351	0.87[ASW][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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2278812	MED13	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60017800-60050400	Strong transcription	Adipose Nuclei	Adipose
2	chr17:60018000-60046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr17:60018000-60072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr17:60018000-60073400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:60018600-60047000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:60018600-60047200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:60018600-60072600	Strong transcription	Fetal Thymus	thymus
8	chr17:60018800-60073600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr17:60019200-60051600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr17:60019600-60050600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:60020200-60050400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr17:60020400-60050600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:60020400-60073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:60020600-60043400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:60020600-60047200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:60020600-60073000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:60020800-60051800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr17:60020800-60073800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:60021000-60047600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:60021000-60050200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr17:60021200-60043600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:60021200-60097000	Strong transcription	Dnd41	blood
23	chr17:60021800-60052400	Strong transcription	HepG2	liver
24	chr17:60021800-60073600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr17:60022000-60043000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:60022000-60051800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr17:60022200-60044200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr17:60022200-60052200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr17:60022200-60053200	Strong transcription	Fetal Intestine Large	intestine
30	chr17:60023000-60043200	Strong transcription	Fetal Muscle Leg	muscle
31	chr17:60023200-60049400	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr17:60023600-60050600	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr17:60025400-60074200	Strong transcription	Liver	Liver
34	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:60026000-60040600	Strong transcription	Lung	lung
36	chr17:60028400-60059600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr17:60030200-60044200	Strong transcription	Thymus	Thymus
38	chr17:60031000-60041400	Weak transcription	Gastric	stomach
39	chr17:60031600-60042400	Weak transcription	Fetal Brain Male	brain
40	chr17:60032600-60041800	Weak transcription	Spleen	Spleen
41	chr17:60032600-60042200	Weak transcription	Psoas Muscle	Psoas
42	chr17:60032800-60042200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr17:60032800-60058600	Weak transcription	Fetal Heart	heart
44	chr17:60033000-60041000	Weak transcription	Brain Hippocampus Middle	brain
45	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
46	chr17:60033200-60041400	Weak transcription	Pancreas	Pancrea
47	chr17:60033200-60042200	Weak transcription	Aorta	Aorta
48	chr17:60033200-60056600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:60034800-60052200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr17:60034800-60072800	Strong transcription	Placenta	Placenta

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