Variant report

Variant	rs7574488
Chromosome Location	chr2:97599618-97599619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:97500023..97502292-chr2:97598667..97600575,2	MCF-7	breast:
2	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
3	chr2:97595378..97599170-chr2:97599205..97602080,3	K562	blood:
4	chr2:97587758..97596829-chr2:97597446..97601811,11	K562	blood:
5	chr2:97588776..97591371-chr2:97597850..97600657,3	MCF-7	breast:
6	chr2:97593614..97595477-chr2:97599029..97600763,2	MCF-7	breast:
7	chr2:97599384..97601746-chr2:97614766..97616556,2	MCF-7	breast:
8	chr2:97590809..97593385-chr2:97597939..97599860,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213337	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11897551	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13393393	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13403225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404734	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13407036	0.86[CEU][hapmap]
rs2872686	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60621865	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7592101	0.85[CEU][hapmap]
rs7594227	0.85[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7603256	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7574488	FAM178B	cis	Esophagus Muscularis	GTEx
rs7574488	LOC375249	cis	multi-tissue	Pritchard
rs7574488		cis	Lymphoblastoid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97594000-97610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:97597200-97606000	Weak transcription	Fetal Thymus	thymus
3	chr2:97598000-97601800	Weak transcription	Right Atrium	heart
4	chr2:97598400-97605800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:97599000-97600200	Enhancers	K562	blood
6	chr2:97599000-97600400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:97599200-97599800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:97599200-97600000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:97599200-97600000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr2:97599200-97600000	Enhancers	Brain Cingulate Gyrus	brain
11	chr2:97599200-97600200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:97599200-97600200	Enhancers	Brain Germinal Matrix	brain
13	chr2:97599200-97600200	Enhancers	Brain Hippocampus Middle	brain
14	chr2:97599200-97600200	Enhancers	Brain Substantia Nigra	brain
15	chr2:97599200-97600200	Enhancers	Fetal Brain Male	brain
16	chr2:97599200-97600400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:97599200-97600600	Enhancers	Fetal Brain Female	brain
18	chr2:97599400-97599800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr2:97599400-97599800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr2:97599400-97600200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:97599600-97600200	Enhancers	Brain Anterior Caudate	brain

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