Variant report

Variant	rs34386102
Chromosome Location	chr4:48484266-48484267
allele	C/T
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	GATA1	chr4:48483478-48484325	K562	blood:	n/a	chr4:48483836-48483848 chr4:48483838-48483845
2	EP300	chr4:48484227-48486994	SK-N-SH	brain:	n/a	chr4:48485456-48485472 chr4:48485429-48485438 chr4:48485459-48485475 chr4:48484359-48484368 chr4:48485366-48485382

No.	Distal block	Cell Line	Cell type
1	chr4:48478979..48481680-chr4:48482843..48484535,2	K562	blood:
2	chr4:48484114..48487251-chr4:48504187..48509460,5	K562	blood:
3	chr4:48341909..48343469-chr4:48483589..48486077,2	K562	blood:
4	chr4:48474711..48478093-chr4:48481760..48484353,3	K562	blood:

Variant related genes	Relation type
SLC10A4	TF binding region
ENSG00000075539	Chromatin interaction
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10517218	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10805169	0.95[EUR][1000 genomes]
rs13102023	0.88[EUR][1000 genomes]
rs13105648	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13110633	0.88[EUR][1000 genomes]
rs13114836	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139251	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13139533	0.91[EUR][1000 genomes]
rs13145713	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1565217	0.82[EUR][1000 genomes]
rs17472127	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34380340	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34922671	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35079648	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35963236	0.85[EUR][1000 genomes]
rs3811759	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62311260	0.85[EUR][1000 genomes]
rs6447639	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811724	0.80[EUR][1000 genomes]
rs6821909	0.81[EUR][1000 genomes]
rs6824075	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824125	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6844692	0.82[EUR][1000 genomes]
rs6845250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847622	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs745761	0.81[EUR][1000 genomes]
rs7670045	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7676578	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7698564	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv1005268	chr4:48444307-48484389	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv537086	chr4:48444307-48484389	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv879008	chr4:48473439-48496804	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv879009	chr4:48476539-48494546	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv3421012	chr4:48483395-48487593	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34386102	SLC10A4	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48483400-48484600	Enhancers	K562	blood
2	chr4:48483600-48484400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:48484000-48484800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:48484200-48484600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
5	chr4:48484200-48484600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:48484200-48484800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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