Variant report

Variant	rs4779041
Chromosome Location	chr15:83337059-83337060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83333276..83339216-chr15:83347120..83352194,10	MCF-7	breast:
2	chr15:83332003..83334784-chr15:83336415..83339116,2	K562	blood:
3	chr15:83314624..83317165-chr15:83336308..83338582,2	K562	blood:
4	chr15:83318720..83320314-chr15:83336857..83339244,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259462	Chromatin interaction
ENSG00000214575	Chromatin interaction
ENSG00000103723	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10400906	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10468217	0.92[ASN][1000 genomes]
rs10906984	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1145172	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1145173	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs11631963	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11633829	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11633991	0.84[GIH][hapmap]
rs11635624	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11637433	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11855735	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12148332	0.94[ASN][1000 genomes]
rs12438312	0.95[ASN][1000 genomes]
rs12442686	0.93[ASN][1000 genomes]
rs1259180	0.92[ASN][1000 genomes]
rs1259182	0.97[ASN][1000 genomes]
rs1259183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1267657	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1267658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1267659	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1269134	0.98[ASN][1000 genomes]
rs12911134	0.92[ASN][1000 genomes]
rs12916980	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1313492	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1313493	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431717	0.93[GIH][hapmap]
rs1594511	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17158390	0.99[ASN][1000 genomes]
rs1864699	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2099259	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2278355	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs2567635	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2567636	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2678445	0.88[ASN][1000 genomes]
rs2678448	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28374463	0.95[ASN][1000 genomes]
rs28415133	0.93[ASN][1000 genomes]
rs28667458	0.92[ASN][1000 genomes]
rs2870965	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2870966	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28808991	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34186444	0.99[ASN][1000 genomes]
rs35934048	0.90[ASN][1000 genomes]
rs36109438	0.93[ASN][1000 genomes]
rs3970696	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4778686	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4779032	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4779039	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4779044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4779050	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4779053	0.92[ASN][1000 genomes]
rs4779054	0.83[ASN][1000 genomes]
rs55924160	0.99[ASN][1000 genomes]
rs57181760	0.98[ASN][1000 genomes]
rs6603030	0.91[GIH][hapmap]
rs6603032	0.90[YRI][hapmap]
rs6603033	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs698500	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7165125	0.97[ASN][1000 genomes]
rs7166248	0.92[ASN][1000 genomes]
rs7167880	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7169145	0.81[YRI][hapmap]
rs7171180	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178350	0.96[ASN][1000 genomes]
rs7179695	0.81[YRI][hapmap]
rs7181761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7182394	0.81[YRI][hapmap]
rs7182403	0.99[ASN][1000 genomes]
rs7183881	0.99[ASN][1000 genomes]
rs7494860	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7496954	0.99[ASN][1000 genomes]
rs783520	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs783522	0.99[ASN][1000 genomes]
rs783523	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs783525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs783526	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs783527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs783529	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs783530	0.94[ASN][1000 genomes]
rs783531	0.93[ASN][1000 genomes]
rs783532	0.94[ASN][1000 genomes]
rs783533	0.96[ASN][1000 genomes]
rs783534	0.96[ASN][1000 genomes]
rs783535	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs783536	0.95[ASN][1000 genomes]
rs783537	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783539	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs783540	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs783543	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs783544	0.93[GIH][hapmap]
rs783545	0.92[ASN][1000 genomes]
rs8033106	0.93[GIH][hapmap]
rs803687	0.86[ASN][1000 genomes]
rs803688	0.87[ASN][1000 genomes]
rs803747	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8040293	0.96[ASN][1000 genomes]
rs8043401	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9652567	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1036950	chr15:83245326-83461261	Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1036462	chr15:83245326-83472507	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv34318	chr15:83283555-83453495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1039021	chr15:83283994-83431548	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3493740	chr15:83295897-83458896	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	esv3493739	chr15:83296247-83458846	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	esv3493738	chr15:83296905-83457854	Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	esv3493742	chr15:83296993-83457792	Weak transcription Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv817702	chr15:83299461-83457424	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	esv1808975	chr15:83307574-83360168	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4779041	RASGRF1	cis	cerebellum	SCAN
rs4779041	CPEB1	cis	parietal	SCAN
rs4779041	FAM154B	cis	parietal	SCAN
rs4779041	GOLGA6L10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83327800-83337400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:83328800-83342600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:83331400-83346600	Weak transcription	Fetal Brain Male	brain
4	chr15:83331600-83337800	Strong transcription	Fetal Brain Female	brain
5	chr15:83334200-83337800	Strong transcription	Brain Angular Gyrus	brain
6	chr15:83334600-83342800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:83334800-83344400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:83335000-83337200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:83335200-83349200	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:83335600-83344200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:83335800-83343200	Weak transcription	Brain Anterior Caudate	brain
12	chr15:83336000-83341600	Weak transcription	Brain Germinal Matrix	brain
13	chr15:83336800-83348200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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