Variant report

Variant	rs28378175
Chromosome Location	chr11:71542598-71542599
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10751157	0.84[ASN][1000 genomes]
rs10751158	0.84[ASN][1000 genomes]
rs10792914	0.84[ASN][1000 genomes]
rs10792915	0.84[ASN][1000 genomes]
rs10792951	0.84[ASN][1000 genomes]
rs10792952	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10792964	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10898623	0.84[ASN][1000 genomes]
rs11235020	0.81[ASN][1000 genomes]
rs11235021	0.82[ASN][1000 genomes]
rs11235093	0.84[ASN][1000 genomes]
rs11235192	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11606005	0.83[ASN][1000 genomes]
rs12420318	0.84[EUR][1000 genomes]
rs1806569	0.84[EUR][1000 genomes]
rs1814920	0.83[ASN][1000 genomes]
rs1945051	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2003240	0.86[ASN][1000 genomes]
rs35755503	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36088573	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3819237	0.80[ASN][1000 genomes]
rs3862788	0.84[ASN][1000 genomes]
rs4122047	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4122048	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4245457	0.80[ASN][1000 genomes]
rs4945295	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4945297	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6592380	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7102608	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7107929	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7129417	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7129769	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7944189	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	esv3527986	chr11:71298409-71620955	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv3527987	chr11:71298409-71620955	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv2761682	chr11:71299175-71619923	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv897904	chr11:71316093-71615727	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv972041	chr11:71330518-71615123	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv3369013	chr11:71338874-71612242	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv2758276	chr11:71363639-71657576	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	esv2759836	chr11:71363639-71657576	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv428262	chr11:71363639-71804055	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
11	nsv897905	chr11:71371354-71615727	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv1819073	chr11:71371742-71618164	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv897906	chr11:71386905-71543708	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv897907	chr11:71386905-71549174	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	esv11723	chr11:71498860-71553549	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	esv1804003	chr11:71512115-71563035	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
17	esv2760190	chr11:71513455-71552665	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv11824	chr11:71515433-71603968	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv8837	chr11:71517340-71559915	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
20	esv1794199	chr11:71517609-71550455	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
21	esv1803631	chr11:71521288-71560091	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28378175	FAM86C1	cis	Adipose Subcutaneous	GTEx
rs28378175	FAM86C1	cis	Muscle Skeletal	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71542000-71542600	Enhancers	Fetal Stomach	stomach
2	chr11:71542400-71547800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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