Variant report

Variant	rs4668346
Chromosome Location	chr2:171781772-171781773
allele	A/G
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	RUNX3	chr2:171781513-171781815	GM12878	blood:	n/a	n/a
2	EBF1	chr2:171781497-171781803	GM12878	blood:	n/a	n/a
3	PAX5	chr2:171781510-171781774	GM12878	blood:	n/a	n/a
4	RUNX3	chr2:171781435-171781814	GM12878	blood:	n/a	n/a
5	EBF1	chr2:171781450-171781854	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171774230..171778889-chr2:171780066..171784826,7	K562	blood:
2	chr2:171780184..171782064-chr2:171783769..171787050,3	MCF-7	breast:

Variant related genes	Relation type
GORASP2	TF binding region
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10803853	0.83[EUR][1000 genomes]
rs11686985	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902360	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902369	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12621769	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025033	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859050	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195116	0.93[EUR][1000 genomes]
rs3755124	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770438	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4667667	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668343	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668354	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433264	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6433266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433267	0.82[EUR][1000 genomes]
rs6729847	0.81[EUR][1000 genomes]
rs6731774	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6742564	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6760293	0.81[AMR][1000 genomes]
rs7559136	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560889	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7567927	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585607	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598194	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4668346	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171775000-171784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:171778200-171784800	Weak transcription	Right Ventricle	heart
3	chr2:171778400-171785000	Weak transcription	Right Atrium	heart
4	chr2:171779000-171784600	Weak transcription	Fetal Heart	heart
5	chr2:171779400-171781800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr2:171779600-171781800	ZNF genes & repeats	Dnd41	blood
7	chr2:171779600-171782800	Weak transcription	HepG2	liver
8	chr2:171781000-171784800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:171781200-171784400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:171781200-171784800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:171781200-171784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:171781200-171784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:171781400-171783800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:171781600-171784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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