Variant report

Variant	rs11079460
Chromosome Location	chr17:60086508-60086509
allele	C/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	POLR2A	chr17:60086255-60087317	K562	blood:	n/a	n/a

Variant related genes	Relation type
RN7SL800P	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11658522	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs12936713	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12941152	1.00[YRI][hapmap]
rs12941827	0.84[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12952534	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35841074	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9893015	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11079460	MED13	cis	cerebellum	SCAN
rs11079460	TBX2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60021200-60097000	Strong transcription	Dnd41	blood
2	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
4	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
5	chr17:60048800-60097600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:60050200-60100800	Weak transcription	Small Intestine	intestine
7	chr17:60059000-60088000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:60060400-60086800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr17:60060400-60088000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:60060400-60090600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr17:60060400-60096200	Weak transcription	Fetal Brain Male	brain
12	chr17:60060400-60098800	Weak transcription	Gastric	stomach
13	chr17:60060400-60099800	Weak transcription	Aorta	Aorta
14	chr17:60061600-60099600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:60062400-60106800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr17:60064800-60088200	Weak transcription	Pancreas	Pancrea
17	chr17:60069200-60107600	Weak transcription	Spleen	Spleen
18	chr17:60069400-60087000	Weak transcription	Left Ventricle	heart
19	chr17:60069600-60099000	Weak transcription	Colonic Mucosa	Colon
20	chr17:60069800-60087800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:60070200-60088000	Weak transcription	NHEK	skin
22	chr17:60072200-60087800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:60072400-60087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr17:60072400-60100600	Weak transcription	Right Ventricle	heart
25	chr17:60074600-60088000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
27	chr17:60074800-60086800	Weak transcription	HSMMtube	muscle
28	chr17:60074800-60087400	Weak transcription	Brain Angular Gyrus	brain
29	chr17:60075000-60092800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:60075800-60087600	Weak transcription	Brain Substantia Nigra	brain
31	chr17:60075800-60087600	Weak transcription	Fetal Heart	heart
32	chr17:60075800-60088000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr17:60076000-60087800	Weak transcription	NHLF	lung
35	chr17:60076200-60086800	Weak transcription	Brain Anterior Caudate	brain
36	chr17:60076200-60087400	Weak transcription	Brain Hippocampus Middle	brain
37	chr17:60076200-60087600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
39	chr17:60077400-60088200	Weak transcription	Ovary	ovary
40	chr17:60077800-60099800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr17:60078000-60086600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr17:60079000-60086800	Weak transcription	HUVEC	blood vessel
43	chr17:60079800-60094000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:60080000-60093200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr17:60080000-60094000	Strong transcription	GM12878-XiMat	blood
46	chr17:60080200-60099000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:60080600-60088000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr17:60080800-60087400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr17:60081200-60093000	Strong transcription	Placenta	Placenta
50	chr17:60081400-60096400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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