Variant report

Variant	rs11729503
Chromosome Location	chr4:120003577-120003578
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11098478	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119909	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732628	0.85[ASN][1000 genomes]
rs11734941	0.85[ASN][1000 genomes]
rs12509365	0.82[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs12641581	0.91[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs13101656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2085660	0.91[JPT][hapmap]
rs2100709	0.91[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs4438744	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4472122	0.85[ASN][1000 genomes]
rs4834739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4834740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831924	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766350	0.91[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap]
rs7670862	0.94[ASN][1000 genomes]
rs985875	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11729503	KIAA1109	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120001200-120004000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr4:120002000-120007800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:120002200-120004000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:120002200-120004200	Enhancers	Fetal Heart	heart
5	chr4:120002400-120003600	Enhancers	Fetal Intestine Large	intestine
6	chr4:120002600-120004200	Enhancers	HepG2	liver
7	chr4:120002800-120003600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr4:120002800-120008000	Weak transcription	Fetal Intestine Small	intestine
9	chr4:120003000-120003600	Enhancers	Right Atrium	heart
10	chr4:120003200-120003600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:120003200-120003600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:120003200-120005400	Weak transcription	HSMMtube	muscle
13	chr4:120003400-120004200	Enhancers	A549	lung
14	chr4:120003400-120007400	Weak transcription	Stomach Mucosa	stomach
15	chr4:120003400-120007800	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:120003400-120014200	Weak transcription	Left Ventricle	heart
17	chr4:120003400-120014400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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