Variant report

Variant	rs7178051
Chromosome Location	chr15:79118296-79118297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79117609..79119286-chr15:79163639..79166414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185787	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10083696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10083697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072807	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638020	0.99[EUR][1000 genomes]
rs11856953	0.99[EUR][1000 genomes]
rs12442476	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898292	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898293	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12898392	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12898452	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12898578	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12898712	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899452	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12907065	0.90[EUR][1000 genomes]
rs12909317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12915192	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28513584	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34372090	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3890715	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3971829	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073321	0.88[ASN][1000 genomes]
rs4073322	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4380028	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4387568	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4389112	0.99[EUR][1000 genomes]
rs4389113	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4433781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4468572	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55870734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56076311	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56683682	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58021857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58158830	0.91[ASN][1000 genomes]
rs61043060	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62011001	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62011002	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66813213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66925868	1.00[EUR][1000 genomes]
rs67745769	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164479	0.84[EUR][1000 genomes]
rs7165042	0.84[EUR][1000 genomes]
rs7165075	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7165081	0.84[EUR][1000 genomes]
rs7165733	0.84[EUR][1000 genomes]
rs7165902	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166764	0.84[EUR][1000 genomes]
rs7167056	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7167242	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7167853	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7176187	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7179953	0.82[EUR][1000 genomes]
rs7181432	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs7182103	0.92[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs7182529	0.84[EUR][1000 genomes]
rs7182716	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs72749206	0.99[EUR][1000 genomes]
rs7402370	0.91[ASN][1000 genomes]
rs7403593	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7403608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7403708	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7403714	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7403728	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8026598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8027833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035093	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8041389	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806363	1.00[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];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9920493	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9920968	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7178051	PSMA4	cis	parietal	SCAN
rs7178051	CTSH	cis	multi-tissue	Pritchard
rs7178051	CTSH	cis	lymphoblastoid	seeQTL
rs7178051	CPLX3	cis	cerebellum	SCAN
rs7178051	CLK3	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79110800-79122600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:79116600-79118800	Enhancers	Ovary	ovary
3	chr15:79116600-79120200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr15:79116800-79118600	Enhancers	Fetal Brain Male	brain
5	chr15:79116800-79120200	Enhancers	HepG2	liver
6	chr15:79117000-79118400	Enhancers	Stomach Smooth Muscle	stomach
7	chr15:79117400-79118400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:79117600-79118400	Enhancers	Fetal Stomach	stomach
9	chr15:79117600-79118400	Enhancers	Rectal Smooth Muscle	rectum
10	chr15:79117600-79118400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr15:79117600-79118600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr15:79117600-79118600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:79117600-79118600	Enhancers	Fetal Lung	lung
14	chr15:79117600-79118800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:79117800-79118400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:79117800-79118400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:79117800-79118400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr15:79117800-79118400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr15:79117800-79118400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:79117800-79118400	Enhancers	Colon Smooth Muscle	Colon
21	chr15:79117800-79118400	Enhancers	Lung	lung
22	chr15:79117800-79118400	Enhancers	Right Atrium	heart
23	chr15:79117800-79118400	Enhancers	Spleen	Spleen
24	chr15:79117800-79118400	Enhancers	HSMMtube	muscle
25	chr15:79117800-79118400	Enhancers	NHLF	lung
26	chr15:79117800-79118600	Enhancers	Liver	Liver
27	chr15:79117800-79118600	Enhancers	Osteobl	bone
28	chr15:79117800-79118800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:79117800-79118800	Enhancers	Fetal Muscle Leg	muscle
30	chr15:79117800-79118800	Enhancers	Left Ventricle	heart
31	chr15:79117800-79118800	Enhancers	NHDF-Ad	bronchial
32	chr15:79117800-79119600	Enhancers	Fetal Muscle Trunk	muscle
33	chr15:79118000-79118400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:79118000-79118400	Enhancers	Fetal Brain Female	brain
35	chr15:79118000-79118400	Enhancers	Fetal Kidney	kidney
36	chr15:79118000-79118400	Enhancers	Right Ventricle	heart
37	chr15:79118000-79118400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr15:79118200-79118400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr15:79118200-79118400	Enhancers	Pancreas	Pancrea
40	chr15:79118200-79118600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr15:79118200-79118600	Enhancers	GM12878-XiMat	blood

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