Variant report

Variant	rs3123541
Chromosome Location	chr1:212816882-212816883
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr1:212816474-212816927	HCT-116	colon:	n/a	n/a
2	USF1	chr1:212816399-212816882	HCT-116	colon:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212731186..212732760-chr1:212816538..212818600,2	K562	blood:
2	chr1:212816407..212819335-chr1:212838741..212840646,2	MCF-7	breast:
3	chr1:212816188..212818854-chr1:212818916..212822054,3	K562	blood:
4	chr1:212814589..212817462-chr1:212838338..212841105,2	K562	blood:
5	chr1:212816188..212818659-chr1:212819327..212822364,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226036	TF binding region
ENSG00000237980	Chromatin interaction
ENSG00000226036	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12143644	0.86[JPT][hapmap]
rs17019532	0.86[JPT][hapmap]
rs17019541	0.86[JPT][hapmap]
rs2501842	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs3003486	0.85[ASN][1000 genomes]
rs3122716	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3123534	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3123537	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3123539	0.81[LWK][hapmap];0.88[MKK][hapmap]
rs3123542	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3125298	0.93[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3125299	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3125300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3125301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6674102	0.93[JPT][hapmap]

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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3123541	KCNH1	cis	parietal	SCAN
rs3123541	PIGR	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212802600-212822800	Weak transcription	Fetal Kidney	kidney
2	chr1:212812400-212821800	Weak transcription	Fetal Lung	lung
3	chr1:212812800-212817400	Weak transcription	Thymus	Thymus
4	chr1:212812800-212819200	Weak transcription	Lung	lung
5	chr1:212813000-212817200	Weak transcription	Fetal Thymus	thymus
6	chr1:212814200-212818000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:212814200-212821800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:212815800-212818200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:212816000-212817200	Weak transcription	Left Ventricle	heart
10	chr1:212816600-212820400	Enhancers	Fetal Intestine Small	intestine
11	chr1:212816800-212820600	Enhancers	Fetal Intestine Large	intestine
12	chr1:212816800-212821000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links