Variant report

Variant	rs62475040
Chromosome Location	chr7:121059553-121059554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:121054365..121057910-chr7:121059475..121061785,3	K562	blood:
2	chr7:121059489..121061007-chr7:121064201..121066957,2	K562	blood:
3	chr7:121034569..121037516-chr7:121059482..121062540,3	MCF-7	breast:
4	chr7:121034886..121037643-chr7:121057416..121062764,7	MCF-7	breast:
5	chr7:121054965..121059361-chr7:121059382..121061611,4	K562	blood:

Variant related genes	Relation type
ENSG00000196937	Chromatin interaction
ENSG00000227371	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10215001	0.85[EUR][1000 genomes]
rs10215613	0.85[EUR][1000 genomes]
rs10215690	0.85[EUR][1000 genomes]
rs10215696	0.84[EUR][1000 genomes]
rs10224285	0.89[EUR][1000 genomes]
rs10224531	0.85[EUR][1000 genomes]
rs10229623	0.85[EUR][1000 genomes]
rs10240942	0.83[EUR][1000 genomes]
rs10255192	0.85[EUR][1000 genomes]
rs10259018	0.85[EUR][1000 genomes]
rs10267770	0.85[EUR][1000 genomes]
rs10270768	0.85[EUR][1000 genomes]
rs11520945	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11521035	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11521036	0.93[EUR][1000 genomes]
rs12706345	0.81[EUR][1000 genomes]
rs12706347	0.85[EUR][1000 genomes]
rs12706348	0.85[EUR][1000 genomes]
rs12706349	0.81[EUR][1000 genomes]
rs13237689	0.83[EUR][1000 genomes]
rs1406191	0.81[EUR][1000 genomes]
rs1534521	0.81[EUR][1000 genomes]
rs1534522	0.85[EUR][1000 genomes]
rs1609291	0.92[EUR][1000 genomes]
rs1881373	0.85[EUR][1000 genomes]
rs2049703	0.85[EUR][1000 genomes]
rs2141359	0.81[EUR][1000 genomes]
rs2178187	0.81[EUR][1000 genomes]
rs2244845	0.85[EUR][1000 genomes]
rs2244847	0.84[EUR][1000 genomes]
rs2244849	0.84[EUR][1000 genomes]
rs2263404	0.85[EUR][1000 genomes]
rs2402564	0.82[EUR][1000 genomes]
rs2402565	0.85[EUR][1000 genomes]
rs2402566	0.85[EUR][1000 genomes]
rs2402567	0.81[EUR][1000 genomes]
rs2463646	0.85[EUR][1000 genomes]
rs2697168	0.85[EUR][1000 genomes]
rs2697171	0.85[EUR][1000 genomes]
rs2697172	0.85[EUR][1000 genomes]
rs2697173	0.85[EUR][1000 genomes]
rs2697174	0.85[EUR][1000 genomes]
rs2697188	0.85[EUR][1000 genomes]
rs2697189	0.84[EUR][1000 genomes]
rs2707484	0.81[EUR][1000 genomes]
rs2707490	0.83[EUR][1000 genomes]
rs2707502	0.84[EUR][1000 genomes]
rs28609751	0.81[EUR][1000 genomes]
rs28623616	0.86[EUR][1000 genomes]
rs2950813	0.85[EUR][1000 genomes]
rs2952573	0.85[EUR][1000 genomes]
rs2952575	0.85[EUR][1000 genomes]
rs2952577	0.83[EUR][1000 genomes]
rs4541839	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4731012	0.85[EUR][1000 genomes]
rs4731015	0.81[EUR][1000 genomes]
rs56403550	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62475037	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62475038	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62475039	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62476180	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62476184	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62476187	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62476208	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62476209	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62476210	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62476211	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6466785	0.85[EUR][1000 genomes]
rs6961822	0.85[EUR][1000 genomes]
rs6962156	0.85[EUR][1000 genomes]
rs7776617	0.90[EUR][1000 genomes]
rs7792145	0.83[EUR][1000 genomes]
rs7794700	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7795121	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7809856	0.85[EUR][1000 genomes]
rs7809875	0.89[EUR][1000 genomes]
rs9641666	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9656282	0.85[EUR][1000 genomes]
rs9656283	0.85[EUR][1000 genomes]
rs9656284	0.85[EUR][1000 genomes]
rs9656285	0.85[EUR][1000 genomes]
rs9886342	0.84[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	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers 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
4	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers 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	nsv428507	chr7:121037303-121191934	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62475040	FAM3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:121056800-121065800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:121058000-121062200	Enhancers	Fetal Intestine Small	intestine
3	chr7:121058800-121062000	Enhancers	Fetal Intestine Large	intestine
4	chr7:121059400-121059600	Enhancers	Duodenum Mucosa	Duodenum
5	chr7:121059400-121060200	Bivalent Enhancer	Stomach Mucosa	stomach
6	chr7:121059400-121060400	Enhancers	Pancreas	Pancrea
7	chr7:121059400-121061800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:121059400-121062200	Enhancers	Placenta	Placenta

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