Variant report

Variant	rs34532258
Chromosome Location	chr2:171784262-171784263
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:171772485..171776882-chr2:171782682..171785818,4	MCF-7	breast:
2	chr2:171784160..171787954-chr2:172288133..172292253,10	K562	blood:
3	chr2:171783060..171786005-chr2:216876902..216878903,2	MCF-7	breast:
4	chr2:171626961..171629009-chr2:171784250..171787377,4	K562	blood:
5	chr2:171774230..171778889-chr2:171780066..171784826,7	K562	blood:
6	chr2:171770723..171773648-chr2:171784124..171786319,2	K562	blood:
7	chr2:171784119..171787322-chr2:172288781..172292051,4	MCF-7	breast:
8	chr2:171783791..171787349-chr2:172286549..172291928,9	K562	blood:
9	chr2:171627023..171629009-chr2:171784250..171786840,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TLK1-3	chr2:171784208-171785364	NONHSAT075436

No data

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000118242	Chromatin interaction
ENSG00000239467	Chromatin interaction
ENSG00000266020	Chromatin interaction
ENSG00000234350	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1045327	0.81[ASN][1000 genomes]
rs10515934	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803853	0.88[ASN][1000 genomes]
rs10803854	0.82[ASN][1000 genomes]
rs10930446	0.81[ASN][1000 genomes]
rs10930448	0.82[ASN][1000 genomes]
rs10930449	0.82[ASN][1000 genomes]
rs11896607	0.85[ASN][1000 genomes]
rs12471930	0.82[ASN][1000 genomes]
rs12612871	0.82[ASN][1000 genomes]
rs12996518	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13000644	0.81[ASN][1000 genomes]
rs13011011	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13015226	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13028857	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13035460	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1529391	0.82[ASN][1000 genomes]
rs1541781	0.81[ASN][1000 genomes]
rs16859066	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17281735	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2195116	0.85[ASN][1000 genomes]
rs34005022	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34330182	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34342928	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34911788	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35123411	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35230775	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35279794	0.83[ASN][1000 genomes]
rs35890547	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3755125	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770440	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770441	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770442	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821090	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233833	0.81[ASN][1000 genomes]
rs4667666	0.81[ASN][1000 genomes]
rs4668355	0.82[ASN][1000 genomes]
rs6433267	0.88[ASN][1000 genomes]
rs6714300	0.82[ASN][1000 genomes]
rs6715386	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724493	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6729847	0.88[ASN][1000 genomes]
rs6742797	0.82[ASN][1000 genomes]
rs6758331	0.83[ASN][1000 genomes]
rs71415229	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71415231	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71415232	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71415233	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731692	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731693	0.82[ASN][1000 genomes]
rs73976229	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7560889	0.82[EUR][1000 genomes]
rs7570701	0.82[ASN][1000 genomes]
rs919190	0.85[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
rs34532258	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 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	chr2:171781000-171784800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:171781200-171784400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:171781200-171784800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:171781200-171784800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:171781200-171784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:171781600-171784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:171781800-171784400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:171782800-171784400	Enhancers	HepG2	liver
13	chr2:171783000-171784400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:171783800-171784800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:171783800-171785200	Flanking Active TSS	Dnd41	blood
16	chr2:171784000-171784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:171784200-171784400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr2:171784200-171784400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr2:171784200-171784400	Enhancers	A549	lung
20	chr2:171784200-171784400	Enhancers	HMEC	breast

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