Variant report

Variant	rs7804178
Chromosome Location	chr7:48122193-48122194
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48121862..48125599-chr7:48127472..48129866,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183696	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10278152	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11768083	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13227958	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13240650	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1554494	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1581415	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1581416	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686796	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2686800	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686802	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686803	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708866	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708867	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708868	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708869	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708870	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708871	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752889	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3752890	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3763504	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763505	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59688958	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62447120	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6968763	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7341420	0.93[ASW][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap]
rs7385009	0.81[AFR][1000 genomes]
rs7458962	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7459020	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7793905	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794100	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639019	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9639991	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1027414	chr7:48117684-48438543	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7804178	ABCA13	cis	parietal	SCAN
rs7804178	UPP1	cis	multi-tissue	Pritchard
rs7804178	UPP1	cis	Muscle Skeletal	GTEx
rs7804178	UPP1	cis	cerebellum	SCAN
rs7804178	PKD1L1	cis	cerebellum	SCAN
rs7804178	PKD1L1	cis	parietal	SCAN
rs7804178	LOC100129427	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48110000-48124200	Weak transcription	Aorta	Aorta
2	chr7:48111200-48127600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:48114200-48122200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:48114400-48122600	Weak transcription	Stomach Mucosa	stomach
5	chr7:48114400-48122800	Weak transcription	Esophagus	oesophagus
6	chr7:48114600-48122600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:48117800-48122400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:48117800-48122800	Weak transcription	Spleen	Spleen
9	chr7:48118600-48122400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:48118600-48122600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr7:48118600-48122800	Weak transcription	Fetal Heart	heart
12	chr7:48119800-48122400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr7:48119800-48122600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:48119800-48124000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr7:48119800-48124000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr7:48120200-48124200	Enhancers	NHEK	skin
17	chr7:48121600-48122800	Enhancers	Hela-S3	cervix
18	chr7:48121600-48124400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:48121600-48125400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:48121800-48122200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:48122000-48122400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:48122000-48123600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr7:48122000-48127800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr7:48122000-48128000	Enhancers	HMEC	breast

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