Variant report

Variant	rs4075453
Chromosome Location	chr6:166722467-166722468
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	GATA3	chr6:166722349-166723173	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:166722438-166722484	ProgFib	skin:	n/a	n/a
3	E2F6	chr6:166720374-166722522	H1-hESC	embryonic stem cell:	n/a	chr6:166722231-166722243 chr6:166722235-166722242 chr6:166722235-166722242 chr6:166722235-166722242 chr6:166721978-166721988
4	TBL1XR1	chr6:166722066-166722548	GM12878	blood:	n/a	n/a
5	MAX	chr6:166721836-166722471	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:166721701-166722482	GM12892	blood:	n/a	n/a
7	EBF1	chr6:166721783-166722517	GM12878	blood:	n/a	chr6:166722139-166722149 chr6:166722140-166722151 chr6:166722140-166722149
8	RUNX3	chr6:166721848-166722468	GM12878	blood:	n/a	n/a
9	GATA3	chr6:166722265-166722979	MCF-7	breast:	n/a	n/a
10	POLR2A	chr6:166721640-166722837	GM12891	blood:	n/a	n/a
11	PML	chr6:166721482-166722537	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166719852..166722547-chr6:166755922..166758056,2	K562	blood:
2	chr6:166722256..166724406-chr6:166752301..166754007,2	MCF-7	breast:

Variant related genes	Relation type
PRR18	TF binding region
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13205770	0.90[EUR][1000 genomes]
rs4075452	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9347122	0.89[ASN][1000 genomes]
rs9348117	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv886935	chr6:166704744-166726566	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv886936	chr6:166714024-166731289	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv823927	chr6:166719837-166722561	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3421182	chr6:166720387-166722935	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4075453	PRR18	cis	lymphoblastoid	seeQTL
rs4075453	FGFR1OP	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166718800-166722600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:166720400-166722600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:166720400-166722600	Active TSS	Brain Angular Gyrus	brain
4	chr6:166720600-166723000	Flanking Active TSS	Liver	Liver
5	chr6:166720800-166722600	Active TSS	Brain Hippocampus Middle	brain
6	chr6:166721000-166722600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:166722000-166722600	Bivalent Enhancer	Fetal Heart	heart
8	chr6:166722000-166723000	Enhancers	Gastric	stomach
9	chr6:166722200-166722600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr6:166722200-166722800	Weak transcription	Right Atrium	heart
11	chr6:166722200-166723000	Flanking Bivalent TSS/Enh	HepG2	liver
12	chr6:166722400-166722600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr6:166722400-166722600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr6:166722400-166722600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr6:166722400-166722600	Active TSS	GM12878-XiMat	blood
16	chr6:166722400-166722800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
17	chr6:166722400-166722800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr6:166722400-166722800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
19	chr6:166722400-166723000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr6:166722400-166723000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:166722400-166723000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:166722400-166723000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr6:166722400-166723000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:166722400-166723000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:166722400-166723000	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr6:166722400-166723000	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr6:166722400-166723200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:166722400-166723200	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr6:166722400-166723200	Bivalent Enhancer	Fetal Intestine Large	intestine
30	chr6:166722400-166723400	Bivalent Enhancer	Fetal Intestine Small	intestine
31	chr6:166722400-166723800	Enhancers	Brain Cingulate Gyrus	brain

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