Variant report

Variant	rs6784404
Chromosome Location	chr3:141073675-141073676
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141069302..141073893-chr3:141077867..141081931,7	K562	blood:
2	chr3:141071211..141074969-chr3:141075130..141079679,8	K562	blood:
3	chr3:141069422..141074358-chr3:141084298..141087585,4	MCF-7	breast:
4	chr3:141070925..141073328-chr3:141073494..141076643,3	MCF-7	breast:
5	chr3:141065346..141067226-chr3:141073466..141076149,2	K562	blood:
6	chr3:141062498..141065026-chr3:141073519..141075054,2	K562	blood:
7	chr3:141030231..141032200-chr3:141070469..141074049,3	K562	blood:
8	chr3:141071983..141074032-chr3:141086697..141088829,2	K562	blood:
9	chr3:141062169..141064184-chr3:141073494..141075542,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13098180	0.83[EUR][1000 genomes]
rs1346408	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16851367	0.83[ASN][1000 genomes]
rs1863868	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2311847	0.84[ASN][1000 genomes]
rs4683603	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440001	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440006	0.81[CEU][hapmap]
rs6781636	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7613516	0.92[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7624084	0.85[CEU][hapmap]
rs9866391	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv460871	chr3:141027614-141074962	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv591893	chr3:141027614-141074962	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	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
rs6784404	ATP1B3	cis	cerebellum	SCAN
rs6784404	RASA2	cis	cerebellum	SCAN
rs6784404	SPSB4	cis	parietal	SCAN

Chromatin state (count:18 , 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	chr3:141066600-141079200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:141066800-141079000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:141067800-141079400	Weak transcription	NHLF	lung
8	chr3:141070200-141075600	Genic enhancers	Fetal Intestine Small	intestine
9	chr3:141070600-141079000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:141071800-141073800	Enhancers	NHEK	skin
11	chr3:141071800-141075400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:141072000-141073800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:141072600-141073800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:141072600-141075200	Enhancers	K562	blood
15	chr3:141073200-141073800	Bivalent Enhancer	Esophagus	oesophagus
16	chr3:141073200-141074600	Enhancers	Placenta	Placenta
17	chr3:141073400-141078200	Strong transcription	Fetal Intestine Large	intestine
18	chr3:141073600-141079000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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