Variant report

Variant	rs4426170
Chromosome Location	chr12:48813318-48813319
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	chr12:48743174..48745194-chr12:48812866..48814557,2	K562	blood:

Variant related genes	Relation type
ENSG00000167528	Chromatin interaction
ENSG00000257735	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11168613	0.80[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12578360	0.82[EUR][1000 genomes]
rs12580814	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs12580859	0.81[EUR][1000 genomes]
rs12581223	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12582586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12582594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17234937	1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2705127	1.00[JPT][hapmap]
rs28889727	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4397895	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4547144	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs55647233	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs55667337	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55971664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55983865	0.82[EUR][1000 genomes]
rs56034252	0.82[EUR][1000 genomes]
rs56191575	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59337124	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61940763	0.82[EUR][1000 genomes]
rs61940764	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61940766	0.82[EUR][1000 genomes]
rs61940767	0.82[EUR][1000 genomes]
rs61940768	0.82[EUR][1000 genomes]
rs61940776	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61940777	0.82[EUR][1000 genomes]
rs61940779	0.82[EUR][1000 genomes]
rs61940780	0.82[EUR][1000 genomes]
rs61940822	0.81[EUR][1000 genomes]
rs61942785	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61942786	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61942787	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61942812	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61942813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61942816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61942817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61942828	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61942829	0.83[EUR][1000 genomes]
rs61942830	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61942831	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4426170	KCNH3	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48808200-48813400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:48808600-48813800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:48808800-48813800	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:48808800-48816000	Weak transcription	Ovary	ovary
5	chr12:48810200-48813400	Weak transcription	Fetal Lung	lung
6	chr12:48812600-48813600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:48812800-48814000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:48812800-48814400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:48812800-48814600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:48813000-48813400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:48813000-48813600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
12	chr12:48813000-48813600	Enhancers	K562	blood
13	chr12:48813000-48814200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr12:48813200-48813800	Enhancers	Adipose Nuclei	Adipose
15	chr12:48813200-48814600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr12:48813200-48814800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:48813200-48815200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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