Variant report

Variant	rs12603447
Chromosome Location	chr17:45146237-45146238
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	POLR2A	chr17:45146171-45146368	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45145658..45148463-chr17:45161187..45163786,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000262879	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10514915	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11079748	0.93[ASN][1000 genomes]
rs11079750	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11079752	0.91[ASN][1000 genomes]
rs11649887	0.93[ASN][1000 genomes]
rs11654517	0.93[ASN][1000 genomes]
rs11658350	0.91[ASN][1000 genomes]
rs11871052	0.86[ASN][1000 genomes]
rs12939753	0.88[ASN][1000 genomes]
rs12942936	0.95[ASN][1000 genomes]
rs12949929	0.92[ASN][1000 genomes]
rs12950276	0.91[ASN][1000 genomes]
rs12950699	0.91[ASN][1000 genomes]
rs1634260	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007723	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2316331	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2317376	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2873131	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34038545	0.95[ASN][1000 genomes]
rs34314554	0.90[ASN][1000 genomes]
rs34710835	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35721448	0.93[ASN][1000 genomes]
rs4074247	0.86[ASN][1000 genomes]
rs4074249	0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4968253	0.91[ASN][1000 genomes]
rs4968304	0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs56362502	0.82[ASN][1000 genomes]
rs7207418	0.89[ASN][1000 genomes]
rs7214785	0.87[ASN][1000 genomes]
rs7215573	0.91[ASN][1000 genomes]
rs7215903	0.91[ASN][1000 genomes]
rs7215907	0.91[ASN][1000 genomes]
rs7219544	0.91[ASN][1000 genomes]
rs7219899	0.91[ASN][1000 genomes]
rs7220777	0.90[ASN][1000 genomes]
rs7222781	0.91[ASN][1000 genomes]
rs8077021	0.92[ASN][1000 genomes]
rs9889451	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899078	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9911967	0.80[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	esv9886	chr17:45142849-45153796	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12603447	KRT31	cis	parietal	SCAN
rs12603447	GOSR2	cis	cerebellum	SCAN
rs12603447	C17orf53	cis	parietal	SCAN
rs12603447	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs12603447	ZNF354A	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45145000-45146600	Weak transcription	Right Atrium	heart
2	chr17:45145000-45146800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:45145000-45146800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:45145000-45146800	Weak transcription	Right Ventricle	heart
5	chr17:45145000-45146800	Weak transcription	Hela-S3	cervix
6	chr17:45145000-45147200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr17:45145000-45147200	Weak transcription	NH-A	brain
8	chr17:45145000-45147200	Weak transcription	NHDF-Ad	bronchial
9	chr17:45145000-45147400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:45145000-45147400	Weak transcription	Stomach Mucosa	stomach
11	chr17:45145000-45147400	Weak transcription	K562	blood
12	chr17:45145000-45147400	Weak transcription	Osteobl	bone
13	chr17:45145000-45147600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:45145000-45147800	Weak transcription	Fetal Thymus	thymus
15	chr17:45145000-45148000	Weak transcription	Liver	Liver
16	chr17:45145000-45148000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr17:45145000-45148200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr17:45145000-45148200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:45145000-45148200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr17:45145000-45148400	Weak transcription	Adipose Nuclei	Adipose
21	chr17:45145000-45148400	Weak transcription	Colonic Mucosa	Colon
22	chr17:45145000-45148600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr17:45145000-45148600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr17:45145000-45148600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr17:45145000-45148600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:45145000-45148600	Weak transcription	Left Ventricle	heart
27	chr17:45145000-45148800	Weak transcription	Fetal Intestine Large	intestine
28	chr17:45145000-45149400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:45145000-45149400	Weak transcription	Fetal Stomach	stomach
30	chr17:45145000-45149400	Weak transcription	Ovary	ovary
31	chr17:45145000-45149400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr17:45145000-45149800	Weak transcription	Spleen	Spleen
33	chr17:45145000-45150000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr17:45145000-45150000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr17:45145000-45150000	Weak transcription	Esophagus	oesophagus
36	chr17:45145000-45150000	Weak transcription	HSMM	muscle
37	chr17:45145000-45150200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr17:45145000-45150200	Weak transcription	Brain Hippocampus Middle	brain
39	chr17:45145000-45151600	Weak transcription	Psoas Muscle	Psoas
40	chr17:45145000-45152200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr17:45145000-45152400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:45145000-45158800	Weak transcription	NHLF	lung
43	chr17:45145000-45163600	Weak transcription	Aorta	Aorta
44	chr17:45145000-45163800	Weak transcription	Small Intestine	intestine
45	chr17:45145000-45164600	Weak transcription	Brain Angular Gyrus	brain
46	chr17:45145000-45169800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:45145000-45169800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:45145000-45169800	Weak transcription	Fetal Lung	lung
49	chr17:45145000-45176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:45145000-45176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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