Variant report

Variant	rs17078988
Chromosome Location	chr5:178459283-178459284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178450567..178452511-chr5:178457855..178459672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234284	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10479519	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10479520	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516149	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10516150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505147	0.82[ASN][1000 genomes]
rs11951738	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11958355	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152869	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160086	0.86[ASN][1000 genomes]
rs13161528	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188724	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13359549	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359570	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359572	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361077	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17078991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969025	0.86[GIH][hapmap]
rs2047354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132671	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132672	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34431447	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34881171	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35568336	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797615	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4700780	1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs4700781	0.88[ASN][1000 genomes]
rs4701030	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4701045	0.88[ASN][1000 genomes]
rs58827878	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60061283	0.90[ASN][1000 genomes]
rs60073676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62393072	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393074	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393075	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62393076	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6601007	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601010	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs6859576	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859767	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6860309	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861539	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867119	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6867208	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868893	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875473	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875622	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888539	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6888567	0.89[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6890317	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6891216	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7707587	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708743	0.92[ASN][1000 genomes]
rs7709054	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711420	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7732719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17078988	ZNF879	cis	lymphoblastoid	seeQTL
rs17078988	SRPX	trans	multi-tissue	Pritchard
rs17078988	RAB24	cis	parietal	SCAN
rs17078988	VNN1	trans	lymphoblastoid	seeQTL
rs17078988	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178451200-178461800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr5:178451400-178461800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:178451600-178460600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr5:178451600-178461400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:178451600-178461800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr5:178451800-178460800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:178451800-178461800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:178451800-178461800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:178451800-178464000	ZNF genes & repeats	Liver	Liver
10	chr5:178453000-178461000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
11	chr5:178453000-178461000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr5:178453000-178461800	ZNF genes & repeats	Brain Anterior Caudate	brain
13	chr5:178453000-178464000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr5:178453200-178460800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr5:178453200-178460800	ZNF genes & repeats	Primary T cells from cord blood	blood
16	chr5:178453200-178461000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
17	chr5:178453200-178461200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr5:178453200-178461200	ZNF genes & repeats	Fetal Kidney	kidney
19	chr5:178453200-178461800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr5:178453200-178461800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
21	chr5:178453200-178461800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:178453200-178461800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
23	chr5:178453200-178461800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
24	chr5:178453200-178462400	ZNF genes & repeats	Fetal Brain Female	brain
25	chr5:178453400-178460600	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr5:178453400-178460800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
27	chr5:178453400-178461600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr5:178453600-178461200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
29	chr5:178453600-178461600	ZNF genes & repeats	Brain Germinal Matrix	brain
30	chr5:178453600-178461600	ZNF genes & repeats	Brain Substantia Nigra	brain
31	chr5:178453600-178461800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
32	chr5:178453600-178462000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr5:178453600-178464200	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr5:178453600-178465800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
35	chr5:178453800-178460400	ZNF genes & repeats	Ovary	ovary
36	chr5:178453800-178460400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
37	chr5:178453800-178461600	ZNF genes & repeats	Brain Angular Gyrus	brain
38	chr5:178453800-178461800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:178453800-178461800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr5:178453800-178461800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
41	chr5:178453800-178462800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:178454000-178460600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:178454000-178461600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
44	chr5:178454000-178461600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
45	chr5:178454000-178461800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
46	chr5:178454000-178461800	ZNF genes & repeats	Colon Smooth Muscle	Colon
47	chr5:178454000-178461800	ZNF genes & repeats	Fetal Brain Male	brain
48	chr5:178454000-178461800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
49	chr5:178454000-178462000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
50	chr5:178454000-178462000	ZNF genes & repeats	Brain Hippocampus Middle	brain

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