Variant report

Variant	rs7676736
Chromosome Location	chr4:103937886-103937887
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103936656..103938160-chr4:103938178..103941059,2	MCF-7	breast:
2	chr4:103747527..103750862-chr4:103937830..103941231,4	MCF-7	breast:
3	chr4:103937535..103939748-chr4:103948954..103951628,2	MCF-7	breast:
4	chr4:103929312..103930892-chr4:103937396..103939916,2	MCF-7	breast:
5	chr4:103933603..103935438-chr4:103936605..103938831,2	K562	blood:
6	chr4:103421593..103424113-chr4:103937527..103940611,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000164037	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10004342	0.81[ASN][1000 genomes]
rs10015289	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10029073	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10031181	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10032234	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1080081	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097796	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097797	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722779	0.85[ASN][1000 genomes]
rs11731885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11737544	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11938650	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12500379	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12501737	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12508069	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13113923	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13117110	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13130741	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13144033	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13150426	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1383733	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17033381	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17215211	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2086499	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28367331	0.81[ASN][1000 genomes]
rs28445579	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28636930	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2866417	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28778380	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28845922	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2903284	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34506429	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34725541	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3843441	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3857198	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857199	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857200	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886722	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886723	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3960788	0.97[ASN][1000 genomes]
rs3974478	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3974481	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3974485	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3974599	0.81[EUR][1000 genomes]
rs3974604	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3974605	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3974606	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3974608	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4235409	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4339216	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4382039	0.85[ASN][1000 genomes]
rs4446311	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4455413	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4455415	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4530634	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4533776	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4540048	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4596243	0.90[EUR][1000 genomes]
rs4623004	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4645215	0.84[ASN][1000 genomes]
rs4698864	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4698867	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4698874	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699035	0.87[ASN][1000 genomes]
rs4699037	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699039	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699040	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4699042	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4699044	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699045	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699046	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699047	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699049	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5028609	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533030	0.82[ASN][1000 genomes]
rs6533035	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6533037	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533046	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6533050	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533051	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533052	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810668	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815526	0.84[ASN][1000 genomes]
rs6815540	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818418	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821173	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6821247	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6824070	0.85[ASN][1000 genomes]
rs6828072	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6830193	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6841492	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6842179	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847093	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6847191	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6852141	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6853193	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6856176	0.85[ASN][1000 genomes]
rs724446	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724447	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7375679	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7659468	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7660298	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663876	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7665655	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7672319	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7676943	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7677003	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7678030	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7681002	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7681629	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7682755	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7685399	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7686957	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7687092	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7687707	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7688940	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694724	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7695096	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7697171	0.90[EUR][1000 genomes]
rs7698608	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307280	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9760180	0.85[ASN][1000 genomes]
rs9917919	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9999303	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv461598	chr4:103807720-103953389	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv594978	chr4:103807720-103953389	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv879684	chr4:103887561-103939894	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7676736	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs7676736	LRRC37A15P	cis	lung	GTEx
rs7676736	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs7676736	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs7676736	MANBA	cis	multi-tissue	Pritchard
rs7676736	KRT8P46	cis	lung	GTEx
rs7676736	CISD2	cis	Nerve Tibial	GTEx
rs7676736	CISD2	cis	Esophagus Muscularis	GTEx
rs7676736	CISD2	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103932600-103939600	Weak transcription	HepG2	liver
2	chr4:103933000-103939600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:103933000-103940000	Weak transcription	Right Atrium	heart
4	chr4:103933200-103939800	Weak transcription	NHLF	lung
5	chr4:103933200-103940400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:103933600-103939800	Weak transcription	NHDF-Ad	bronchial
7	chr4:103933800-103938400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:103934000-103939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:103934000-103939200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:103934000-103939800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:103934000-103939800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:103934000-103939800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:103934000-103939800	Weak transcription	Psoas Muscle	Psoas
14	chr4:103934000-103939800	Weak transcription	NHEK	skin
15	chr4:103934200-103939600	Weak transcription	K562	blood
16	chr4:103934200-103939800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:103934200-103939800	Weak transcription	Adipose Nuclei	Adipose
18	chr4:103934200-103939800	Weak transcription	Brain Substantia Nigra	brain
19	chr4:103934200-103939800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:103934200-103940200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:103934400-103939600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:103934400-103940000	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:103934600-103938400	Weak transcription	Hela-S3	cervix
24	chr4:103934600-103939800	Weak transcription	Brain Anterior Caudate	brain
25	chr4:103935600-103939000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:103936800-103940200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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