Variant report

Variant	rs2346878
Chromosome Location	chr2:46922870-46922871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:46922333-46922951	HCT-116	colon:	n/a	chr2:46922652-46922661 chr2:46922434-46922443 chr2:46922586-46922596
2	CBX3	chr2:46922315-46922888	HCT-116	colon:	n/a	n/a
3	NFIC	chr2:46922333-46923033	SK-N-SH	brain:	n/a	chr2:46922695-46922712
4	FOSL1	chr2:46922316-46922962	HCT-116	colon:	n/a	chr2:46922651-46922660 chr2:46922652-46922661
5	FOSL1	chr2:46922318-46922958	HCT-116	colon:	n/a	chr2:46922651-46922660 chr2:46922652-46922661

No.	Distal block	Cell Line	Cell type
1	chr2:46897133..46898995-chr2:46922668..46925477,2	K562	blood:
2	chr2:46919753..46923455-chr2:46923473..46925760,5	K562	blood:
3	chr2:46919532..46921625-chr2:46922624..46924303,3	MCF-7	breast:
4	chr2:46920025..46923233-chr2:46925972..46929255,3	K562	blood:
5	chr2:46921129..46924889-chr2:46924933..46928761,3	MCF-7	breast:
6	chr2:46921430..46924294-chr2:46954187..46957185,2	MCF-7	breast:

Variant related genes	Relation type
SOCS5	TF binding region
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1058157	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1109380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676737	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11695058	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12474201	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998753	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12998762	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12999586	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13025595	0.84[AMR][1000 genomes]
rs13025984	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13429704	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17822019	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17822294	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34401107	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35158352	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35722922	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35825831	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3829835	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4952842	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4952843	0.84[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4953419	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6738426	0.82[AMR][1000 genomes]
rs7562173	0.84[AMR][1000 genomes]
rs7584870	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs7594523	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs897530	0.80[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv3365634	chr2:46910377-46929000	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3460455	chr2:46910422-46928955	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3460454	chr2:46910435-46928955	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3460456	chr2:46910436-46928951	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2346878	SOCS5	cis	brain	BrainEAC
rs2346878	SOCS5	cis	temporal cortex	BrainEAC

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46911600-46924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:46918600-46925000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr2:46919200-46924800	Weak transcription	A549	lung
4	chr2:46919200-46925200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:46919200-46925200	Weak transcription	NH-A	brain
6	chr2:46919400-46924800	Weak transcription	Hela-S3	cervix
7	chr2:46919800-46925000	Weak transcription	Osteobl	bone
8	chr2:46920000-46924800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:46920400-46925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:46922400-46923000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:46922600-46924200	Weak transcription	Brain Germinal Matrix	brain
12	chr2:46922600-46925200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:46922600-46925400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:46922800-46924600	Enhancers	HepG2	liver
15	chr2:46922800-46925000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:46922800-46925000	Weak transcription	NHDF-Ad	bronchial
17	chr2:46922800-46925000	Weak transcription	NHEK	skin
18	chr2:46922800-46925000	Weak transcription	NHLF	lung

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