Variant report

Variant	rs34549224
Chromosome Location	chr1:210620779-210620780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210618870..210621785-chr1:211306135..211307908,2	MCF-7	breast:
2	chr1:210545794..210547749-chr1:210620055..210622714,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143473	Chromatin interaction
ENSG00000234233	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11809771	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11810188	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12408887	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016247	0.81[CEU][hapmap]
rs17188288	1.00[YRI][hapmap]
rs17260473	1.00[YRI][hapmap]
rs2003698	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103692	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2206609	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357590	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537555	1.00[YRI][hapmap]
rs4845015	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845017	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845028	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845030	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845031	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56252446	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745472	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72745499	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs742562	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527066	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534912	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534914	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs910030	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910031	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926578	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756883	chr1:210579523-210620779	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	esv2758995	chr1:210579523-210620779	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34549224	KCNH1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210571400-210641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:210592800-210625000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:210611600-210639600	Weak transcription	Aorta	Aorta
4	chr1:210614600-210641200	Weak transcription	Gastric	stomach
5	chr1:210614800-210623800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:210618400-210620800	Enhancers	Thymus	Thymus
7	chr1:210618400-210621400	Genic enhancers	HSMM	muscle
8	chr1:210619000-210620800	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:210619000-210621800	Enhancers	Fetal Thymus	thymus
10	chr1:210619800-210621400	Enhancers	A549	lung
11	chr1:210620000-210622200	Enhancers	HSMMtube	muscle
12	chr1:210620200-210621000	Enhancers	Dnd41	blood
13	chr1:210620200-210621200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:210620200-210621800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:210620200-210622000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:210620200-210622400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:210620200-210637800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:210620400-210621800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:210620400-210623800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:210620400-210626000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:210620600-210621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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