Variant report

Variant	rs3017
Chromosome Location	chr3:53899580-53899581
allele	C/T
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	chr3:53899424-53900537	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53897345..53899772-chr3:53903994..53906102,2	K562	blood:
2	chr3:53897547..53899772-chr3:53903890..53906304,3	K562	blood:
3	chr3:53895286..53896843-chr3:53899099..53900867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271976	TF binding region
ENSG00000113812	Chromatin interaction
ENSG00000271976	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020082	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134091	0.84[EUR][1000 genomes]
rs12632292	0.88[EUR][1000 genomes]
rs17053568	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17053590	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs1982171	0.81[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241806	0.81[CEU][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2276840	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276843	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276844	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276845	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289203	0.81[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2304575	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304576	0.81[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs2884631	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733075	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3733079	0.81[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733083	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821868	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821869	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292476	0.83[EUR][1000 genomes]
rs4141606	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs45511795	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687594	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs4687753	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687756	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4687758	0.81[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55917919	0.80[EUR][1000 genomes]
rs56743403	0.82[EUR][1000 genomes]
rs57398949	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62253003	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253004	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6445612	0.81[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs709324	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636856	0.81[CEU][hapmap]
rs9840445	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849951	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9850063	0.88[EUR][1000 genomes]
rs9860367	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9880056	0.81[CEU][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs999514	0.81[CEU][hapmap]
rs999515	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3017	IL17RB	cis	parietal	SCAN
rs3017	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs3017	IL17RB	cis	cerebellum	SCAN
rs3017	ACTR8	cis	parietal	SCAN
rs3017	ACTR8	cis	cerebellum	SCAN
rs3017	ACTR8	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53885000-53901000	Weak transcription	Fetal Heart	heart
2	chr3:53888400-53914600	Weak transcription	Stomach Mucosa	stomach
3	chr3:53889000-53901400	Weak transcription	Esophagus	oesophagus
4	chr3:53889600-53913800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:53890000-53904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:53890400-53903600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:53890800-53914600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:53891000-53914200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:53891000-53914200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr3:53891200-53900800	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:53891200-53910800	Strong transcription	Fetal Stomach	stomach
12	chr3:53891400-53914200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:53891600-53904000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:53891800-53912800	Strong transcription	Brain Germinal Matrix	brain
15	chr3:53892000-53914400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:53892200-53912400	Strong transcription	Fetal Brain Female	brain
17	chr3:53892200-53914000	Strong transcription	Adipose Nuclei	Adipose
18	chr3:53892200-53914400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:53892200-53914600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:53892400-53904800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:53892400-53906200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:53892400-53913000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:53892400-53913800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:53892400-53914200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:53892400-53914400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:53892600-53914200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:53892600-53914400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:53892600-53914400	Strong transcription	Fetal Muscle Leg	muscle
29	chr3:53892800-53914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:53892800-53914200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:53892800-53914200	Strong transcription	Thymus	Thymus
32	chr3:53892800-53914400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:53892800-53914600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:53893000-53914000	Strong transcription	Placenta	Placenta
35	chr3:53893000-53914400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:53893200-53914000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:53893200-53914200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:53893200-53914200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr3:53893200-53914200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:53893200-53914600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:53893400-53902600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:53893400-53908200	Weak transcription	K562	blood
43	chr3:53893400-53914200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:53893600-53899800	Weak transcription	Right Atrium	heart
45	chr3:53893800-53912800	Strong transcription	Brain Anterior Caudate	brain
46	chr3:53894200-53900600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:53894200-53914400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:53894400-53899600	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:53894400-53914000	Strong transcription	Primary T cells from cord blood	blood
50	chr3:53894400-53914400	Strong transcription	Fetal Thymus	thymus

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