Variant report

Variant	rs7598661
Chromosome Location	chr2:47468955-47468956
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47465412..47469681-chr2:47474773..47478680,4	MCF-7	breast:
2	chr2:47462369..47466702-chr2:47468560..47470875,4	K562	blood:
3	chr2:47402721..47404828-chr2:47466923..47470052,3	MCF-7	breast:
4	chr2:47399058..47406701-chr2:47458639..47471254,30	K562	blood:
5	chr2:47468738..47470603-chr2:47472163..47473920,2	K562	blood:
6	chr2:47467890..47470603-chr2:47472070..47473663,2	K562	blood:
7	chr2:47406207..47408675-chr2:47468954..47471024,2	MCF-7	breast:
8	chr2:47461484..47463869-chr2:47468560..47470717,2	K562	blood:
9	chr2:47399687..47407797-chr2:47461699..47469642,25	K562	blood:
10	chr2:47464125..47466702-chr2:47468051..47470081,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10169164	0.88[CEU][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1995109	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1995110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4952879	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6748764	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7560679	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs904160	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	esv10649	chr2:47429316-47472670	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
5	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7598661	LOC100129726	cis	parietal	SCAN
rs7598661	STON1-GTF2A1L	cis	parietal	SCAN
rs7598661	ABCG8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47466400-47470800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:47466800-47469200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:47466800-47470800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:47467000-47469600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:47467000-47470800	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:47467000-47471000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:47467000-47476400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:47467200-47469000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:47467200-47470600	Weak transcription	Fetal Stomach	stomach
10	chr2:47467200-47471000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:47467200-47476200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:47467400-47469000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:47467400-47471000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:47467400-47476000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:47467400-47476200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:47468600-47469800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:47468800-47469000	Enhancers	Ovary	ovary
18	chr2:47468800-47469000	Enhancers	Right Atrium	heart
19	chr2:47468800-47469400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:47468800-47469800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:47468800-47469800	Enhancers	K562	blood

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