Variant report

Variant	rs829692
Chromosome Location	chr2:30656281-30656282
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	E2F6	chr2:30656273-30656740	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30656122..30657927-chr2:30882873..30885685,2	K562	blood:

Variant related genes	Relation type
ENSG00000221377	TF binding region

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1036941	0.98[AFR][1000 genomes]
rs11692096	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs11895131	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap]
rs11901266	1.00[YRI][hapmap]
rs1252619	0.98[AFR][1000 genomes]
rs1252627	0.83[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1252635	0.82[CHB][hapmap];0.83[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1662943	0.98[AFR][1000 genomes]
rs1662945	0.98[AFR][1000 genomes]
rs1723172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17395007	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs17395091	0.82[CHB][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1807334	0.82[CHB][hapmap]
rs1869422	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs2253299	0.82[CHB][hapmap]
rs2593445	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2593446	0.82[CHB][hapmap]
rs2593473	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs2602803	0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[YRI][hapmap]
rs2609920	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs57484347	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57637161	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs711236	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs711241	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs829566	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs829567	0.98[AFR][1000 genomes]
rs829568	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs829621	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs829624	0.82[CHB][hapmap];0.87[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs829625	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs829640	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs829643	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs829652	1.00[ASW][hapmap];0.82[CHB][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes]
rs829656	1.00[YRI][hapmap]
rs829674	0.82[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs829676	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs829678	0.93[AFR][1000 genomes]
rs829683	0.82[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs829685	1.00[ASW][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs829688	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829691	0.90[AFR][1000 genomes]
rs829697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs829692	LYCAT	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30645600-30656600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:30645800-30656600	Weak transcription	Fetal Lung	lung
3	chr2:30646400-30656400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:30646400-30662600	Weak transcription	Thymus	Thymus
5	chr2:30647800-30659800	Weak transcription	Left Ventricle	heart
6	chr2:30648600-30659600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:30651600-30656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:30651600-30656600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:30652000-30660800	Weak transcription	K562	blood
10	chr2:30654200-30656600	Weak transcription	Right Atrium	heart
11	chr2:30655400-30656800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:30655400-30656800	Enhancers	Fetal Heart	heart
13	chr2:30655600-30656400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:30655600-30656400	Weak transcription	Osteobl	bone
15	chr2:30655600-30656600	Weak transcription	NHDF-Ad	bronchial
16	chr2:30656200-30657800	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:30656200-30658000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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