Variant report

Variant	rs7613516
Chromosome Location	chr3:141079309-141079310
allele	G/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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141028623..141032743-chr3:141076399..141079995,4	K562	blood:
2	chr3:141058868..141063187-chr3:141079232..141081796,3	K562	blood:
3	chr3:141079302..141080674-chr3:141170565..141171750,10	MCF-7	breast:
4	chr3:141078586..141083082-chr3:141083147..141089245,7	K562	blood:
5	chr3:141078561..141083432-chr3:141083715..141088682,12	MCF-7	breast:
6	chr3:141078321..141083296-chr3:141083518..141088899,11	MCF-7	breast:
7	chr3:141069302..141073893-chr3:141077867..141081931,7	K562	blood:
8	chr3:141075490..141079205-chr3:141079286..141082614,3	K562	blood:
9	chr3:141071211..141074969-chr3:141075130..141079679,8	K562	blood:
10	chr3:141078564..141081479-chr3:141173622..141176571,3	MCF-7	breast:
11	chr3:141078683..141080733-chr3:141115929..141118678,2	MCF-7	breast:
12	chr3:141050275..141052450-chr3:141077492..141079872,2	MCF-7	breast:
13	chr3:141074101..141082527-chr3:141083011..141090165,19	K562	blood:
14	chr3:141078410..141082494-chr3:141170544..141172496,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13098180	0.81[EUR][1000 genomes]
rs1344672	0.81[CEU][hapmap]
rs1344674	0.81[CEU][hapmap]
rs1346408	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1582874	0.81[CEU][hapmap]
rs1863868	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983233	1.00[YRI][hapmap]
rs1991431	0.81[CEU][hapmap]
rs2871887	1.00[YRI][hapmap]
rs2871960	0.81[CEU][hapmap]
rs4683603	0.89[EUR][1000 genomes]
rs6440001	0.81[ASW][hapmap];0.96[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs6440003	0.81[CEU][hapmap]
rs6440006	0.85[CEU][hapmap]
rs6763927	0.81[CEU][hapmap]
rs6763931	0.84[CEU][hapmap]
rs6764769	0.81[CEU][hapmap]
rs6784404	0.92[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6808936	0.81[CEU][hapmap]
rs724016	0.81[CEU][hapmap]
rs7624084	0.93[CEU][hapmap]
rs7632381	0.81[CEU][hapmap]
rs9838625	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs9846396	0.81[CEU][hapmap]
rs9866391	0.89[CEU][hapmap];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7613516	ZBTB38	cis	cerebellum	SCAN
rs7613516	ATP1B3	cis	cerebellum	SCAN
rs7613516	RASA2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141056400-141079400	Weak transcription	A549	lung
2	chr3:141064600-141080400	Weak transcription	Colonic Mucosa	Colon
3	chr3:141065800-141085200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:141066400-141079600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:141067800-141079400	Weak transcription	NHLF	lung
6	chr3:141074600-141079600	Weak transcription	Placenta	Placenta
7	chr3:141075200-141079400	Weak transcription	HUVEC	blood vessel
8	chr3:141075400-141079400	Weak transcription	HepG2	liver
9	chr3:141075400-141079600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:141077000-141079800	Enhancers	K562	blood
11	chr3:141077600-141085400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:141078200-141079600	Genic enhancers	Fetal Intestine Small	intestine
13	chr3:141078200-141079800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:141078400-141079800	Weak transcription	Right Atrium	heart
15	chr3:141079000-141079600	Enhancers	Hela-S3	cervix
16	chr3:141079000-141079800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:141079000-141079800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:141079000-141080000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:141079000-141080400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:141079000-141080800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:141079200-141079800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr3:141079200-141080400	Enhancers	Fetal Intestine Large	intestine

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