Variant report

Variant	rs639342
Chromosome Location	chr5:76112869-76112870
allele	A/G
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	GATA3	chr5:76112650-76113211	SK-N-SH	brain:	n/a	chr5:76112977-76112986 chr5:76113118-76113128 chr5:76113036-76113043
2	REST	chr5:76112815-76113102	PFSK-1	brain:	n/a	chr5:76112988-76113006 chr5:76112987-76113007 chr5:76112987-76112996
3	TCF12	chr5:76111750-76113237	SK-N-SH	brain:	n/a	n/a
4	REST	chr5:76112844-76113099	SK-N-SH	brain:	n/a	chr5:76112988-76113006 chr5:76112987-76113007 chr5:76112987-76112996
5	GATA3	chr5:76112848-76113112	T-47D	breast:	n/a	chr5:76112977-76112986 chr5:76113036-76113043
6	REST	chr5:76112791-76113114	PFSK-1	brain:	n/a	chr5:76112988-76113006 chr5:76112987-76113007 chr5:76112987-76112996
7	GATA3	chr5:76111872-76113336	SK-N-SH	brain:	n/a	chr5:76112977-76112986 chr5:76113118-76113128 chr5:76113036-76113043

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:76110973..76114089-chr5:76116480..76119427,3	K562	blood:
2	chr5:76103612..76107653-chr5:76108707..76113004,3	MCF-7	breast:

Variant related genes	Relation type
F2RL1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2227819	1.00[ASN][1000 genomes]
rs2243018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460498	1.00[ASW][hapmap]
rs59233748	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs636150	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6453267	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs686868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv462213	chr5:76067624-76112869	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv598682	chr5:76067624-76112869	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1015997	chr5:76079720-76129241	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1031491	chr5:76083382-76129241	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2763908	chr5:76083394-76134777	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	5 gene(s)	inside rSNPs	diseases
7	nsv598683	chr5:76086597-76129053	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv882210	chr5:76086597-76140337	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1022431	chr5:76086795-76127170	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1020397	chr5:76086795-76129241	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv598684	chr5:76086795-76130113	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1025151	chr5:76086795-76134777	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025061	chr5:76087544-76129241	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1033086	chr5:76088861-76129241	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1021460	chr5:76089512-76129241	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1018194	chr5:76090951-76129241	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv598685	chr5:76092225-76128521	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv882211	chr5:76100536-76125577	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs639342	CBR3	trans	lymphoblastoid	seeQTL
rs639342	POLK	cis	cerebellum	SCAN
rs639342	NSA2	cis	cerebellum	SCAN
rs639342	F2RL1	cis	Whole Blood	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76102600-76114400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:76105400-76114200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:76108600-76113800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:76109400-76114200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:76109600-76113000	Enhancers	Hela-S3	cervix
6	chr5:76109600-76113200	Enhancers	HMEC	breast
7	chr5:76109600-76114000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:76109600-76114000	Enhancers	NHEK	skin
9	chr5:76109800-76113200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:76110000-76113400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:76110200-76114200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:76110200-76114400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:76110200-76114400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:76110400-76114200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:76110400-76114400	Weak transcription	NHLF	lung
16	chr5:76110600-76114000	Enhancers	A549	lung
17	chr5:76110600-76114000	Weak transcription	NH-A	brain
18	chr5:76110600-76114200	Weak transcription	HUVEC	blood vessel
19	chr5:76112000-76113200	Enhancers	NHDF-Ad	bronchial
20	chr5:76112200-76113000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:76112400-76114400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:76112800-76113000	Enhancers	Osteobl	bone

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