Variant report

Variant	rs1474454
Chromosome Location	chr17:38791481-38791482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38779995..38783555-chr17:38789227..38792857,3	MCF-7	breast:
2	chr17:38791190..38792732-chr17:38799523..38801927,2	MCF-7	breast:
3	chr17:38786790..38789659-chr17:38789846..38792079,3	K562	blood:
4	chr17:38791360..38793414-chr17:38804044..38805611,2	K562	blood:
5	chr17:38789697..38792410-chr17:38802338..38804575,2	MCF-7	breast:
6	chr17:38783257..38785685-chr17:38788764..38791698,3	K562	blood:

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11078950	0.87[EUR][1000 genomes]
rs11650910	0.87[EUR][1000 genomes]
rs11654834	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659024	0.81[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11869540	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1526601	0.90[EUR][1000 genomes]
rs16966093	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961204	0.80[EUR][1000 genomes]
rs2011870	0.87[EUR][1000 genomes]
rs2429547	0.86[EUR][1000 genomes]
rs2429548	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs2429550	0.80[EUR][1000 genomes]
rs2429551	0.95[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs2429552	0.88[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2462957	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs2462960	0.81[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs2462961	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2462965	0.80[EUR][1000 genomes]
rs2462966	0.92[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs2462969	0.92[CEU][hapmap]
rs2469817	0.92[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs2469820	0.92[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs2469825	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs55664118	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503546	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67138687	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7224919	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs723728	0.88[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs723729	0.88[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs726849	0.88[CEU][hapmap]
rs8065040	0.91[EUR][1000 genomes]
rs8066541	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8074179	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8074758	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs874889	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs887376	0.92[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs9303294	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs9630729	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9675112	0.85[CEU][hapmap]
rs9894823	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9902509	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1474454	SPRY2	trans	lymphoblastoid	seeQTL
rs1474454	KRT24	cis	Esophagus Mucosa	GTEx
rs1474454	SMARCE1	cis	multi-tissue	Pritchard
rs1474454	CCL4	cis	parietal	SCAN
rs1474454	TADA2A	cis	cerebellum	SCAN
rs1474454	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs1474454	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38781200-38791600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:38781800-38793600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:38782600-38801000	Strong transcription	Primary B cells from cord blood	blood
4	chr17:38783000-38794000	Strong transcription	Fetal Brain Female	brain
5	chr17:38783000-38800200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr17:38783000-38802400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:38783200-38794200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:38783200-38794400	Strong transcription	NH-A	brain
9	chr17:38783200-38794600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:38783200-38799200	Strong transcription	Fetal Muscle Leg	muscle
11	chr17:38783200-38800600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:38783200-38800800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:38783200-38800800	Strong transcription	GM12878-XiMat	blood
14	chr17:38783200-38801400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr17:38783200-38801400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr17:38783200-38801400	Strong transcription	A549	lung
17	chr17:38783200-38801600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:38783200-38801800	Strong transcription	Fetal Thymus	thymus
19	chr17:38783200-38801800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr17:38783400-38794400	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr17:38783400-38794800	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr17:38783400-38800400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:38783400-38800600	Strong transcription	Primary T cells from cord blood	blood
24	chr17:38783400-38801400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:38783400-38801400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:38783400-38801400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr17:38783400-38801600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr17:38783400-38801600	Strong transcription	Liver	Liver
29	chr17:38783400-38802000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:38783400-38802200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:38783600-38800800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr17:38783600-38801600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr17:38783600-38802400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:38783800-38794200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:38783800-38794200	Strong transcription	Brain Hippocampus Middle	brain
36	chr17:38783800-38796000	Strong transcription	Dnd41	blood
37	chr17:38783800-38801400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr17:38783800-38802800	Strong transcription	Placenta	Placenta
39	chr17:38784000-38793000	Strong transcription	Left Ventricle	heart
40	chr17:38784000-38794600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr17:38784000-38794600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr17:38784000-38794800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr17:38784000-38796000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr17:38784000-38796000	Strong transcription	Adipose Nuclei	Adipose
45	chr17:38784000-38799200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr17:38784000-38801600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr17:38784200-38791600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:38784200-38793000	Strong transcription	Brain Germinal Matrix	brain
49	chr17:38784200-38794400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr17:38784200-38799200	Strong transcription	NHDF-Ad	bronchial

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