Variant report

Variant	rs8074179
Chromosome Location	chr17:38770965-38770966
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38764344..38766277-chr17:38769758..38772025,3	MCF-7	breast:
2	chr17:38770739..38772968-chr17:38952202..38954281,2	MCF-7	breast:
3	chr17:38770013..38773292-chr17:38776635..38779762,4	MCF-7	breast:
4	chr17:38707503..38711120-chr17:38769935..38775644,8	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11654834	0.81[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11659024	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474454	0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs16966093	0.86[ASN][1000 genomes]
rs2429548	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs2429551	0.83[JPT][hapmap]
rs2429552	0.89[CHD][hapmap]
rs2462957	0.82[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs2462960	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs2462961	0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs2462966	0.89[CHD][hapmap];0.82[GIH][hapmap]
rs2469817	0.89[CHD][hapmap]
rs2469820	0.89[CHD][hapmap]
rs2469825	0.82[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs55664118	0.92[ASN][1000 genomes]
rs6503545	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6503546	0.86[ASN][1000 genomes]
rs67138687	0.86[ASN][1000 genomes]
rs7218478	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7224919	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs723728	0.81[GIH][hapmap]
rs723729	0.84[CHD][hapmap]
rs8066541	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8074758	0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap]
rs874889	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs887376	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs9303294	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9630727	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9630729	0.87[ASN][1000 genomes]
rs9894823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9902509	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	esv3361502	chr17:38770953-38771190	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8074179	SMARCE1	cis	multi-tissue	Pritchard
rs8074179	KRT24	cis	Esophagus Mucosa	GTEx
rs8074179	SMARCE1	cis	brain	seeQTL
rs8074179	KRT31	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38763400-38775600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:38764800-38771000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:38768600-38771200	Weak transcription	Thymus	Thymus
4	chr17:38769000-38771200	Enhancers	Primary B cells from peripheral blood	blood
5	chr17:38769000-38772600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:38769200-38771000	Enhancers	GM12878-XiMat	blood
7	chr17:38769200-38771200	Enhancers	Primary B cells from cord blood	blood
8	chr17:38769600-38771200	Weak transcription	Esophagus	oesophagus
9	chr17:38769600-38784200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:38769800-38771200	Weak transcription	Gastric	stomach
11	chr17:38769800-38772800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:38770000-38771000	Enhancers	Primary T cells from cord blood	blood
13	chr17:38770000-38771000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr17:38770000-38771000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr17:38770000-38771000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:38770000-38771200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr17:38770000-38771400	Weak transcription	A549	lung
18	chr17:38770000-38772000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr17:38770000-38773400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr17:38770000-38773600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr17:38770400-38771000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr17:38770400-38771200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr17:38770400-38773600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr17:38770400-38774000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr17:38770600-38772800	Enhancers	Fetal Thymus	thymus
26	chr17:38770600-38774000	Weak transcription	Right Atrium	heart
27	chr17:38770800-38771000	Enhancers	Fetal Kidney	kidney
28	chr17:38770800-38771200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr17:38770800-38771400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:38770800-38771400	Enhancers	Lung	lung
31	chr17:38770800-38771400	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr17:38770800-38772000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr17:38770800-38772400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr17:38770800-38772400	Enhancers	Spleen	Spleen
35	chr17:38770800-38772600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:38770800-38773000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:38770800-38776200	Enhancers	Placenta	Placenta

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