Variant report

Variant	rs60893569
Chromosome Location	chr1:174993370-174993371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:174992142-174993387	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:174992074-174993442	HepG2	liver:	n/a	n/a
3	MTA3	chr1:174991820-174993397	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:174993356-174993682	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:174991898-174993763	K562	blood:	n/a	n/a
6	HCFC1	chr1:174991537-174993387	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:174992131-174993389	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:174992041-174993419	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174992689..174994323-chr17:56736359..56737896,2	MCF-7	breast:
2	chr1:174992825..174995632-chr1:174996081..174999511,5	MCF-7	breast:
3	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
4	chr1:174844676..174846906-chr1:174992717..174994298,2	MCF-7	breast:
5	chr1:174967181..174971270-chr1:174989768..174994107,8	MCF-7	breast:
6	chr1:174763378..174766267-chr1:174992763..174994276,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000206659	TF binding region
MRPS14	TF binding region
ENSG00000152061	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000202077	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10489330	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10489332	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11811190	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12140378	0.94[ASN][1000 genomes]
rs12735946	0.81[EUR][1000 genomes]
rs12737503	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16847730	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861102	0.93[ASN][1000 genomes]
rs35035962	0.81[EUR][1000 genomes]
rs35464086	0.80[EUR][1000 genomes]
rs3737935	0.80[EUR][1000 genomes]
rs3753562	0.83[AFR][1000 genomes]
rs41266060	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41266064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41498747	0.84[AFR][1000 genomes]
rs57053120	0.84[AFR][1000 genomes]
rs58618779	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58762254	0.88[AFR][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	nsv947512	chr1:174984818-175000909	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60893569	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174991600-174993400	Active TSS	Fetal Brain Female	brain
2	chr1:174992000-174993400	Active TSS	Brain Hippocampus Middle	brain
3	chr1:174992000-174993400	Active TSS	Stomach Smooth Muscle	stomach
4	chr1:174992400-174993400	Active TSS	Primary T cells from cord blood	blood
5	chr1:174992800-174993400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:174992800-174993400	Flanking Active TSS	Dnd41	blood
7	chr1:174993000-174993400	Enhancers	Aorta	Aorta
8	chr1:174993000-174993400	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr1:174993000-174993400	Flanking Active TSS	K562	blood
10	chr1:174993200-174993400	Enhancers	Primary B cells from cord blood	blood
11	chr1:174993200-174993400	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:174993200-174993400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:174993200-174993400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:174993200-174993400	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:174993200-174993400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:174993200-174993400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:174993200-174993400	Enhancers	Fetal Thymus	thymus
18	chr1:174993200-174993400	Enhancers	Pancreas	Pancrea
19	chr1:174993200-174993400	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:174993200-174993400	Enhancers	Thymus	Thymus
21	chr1:174993200-174993400	Flanking Active TSS	HepG2	liver
22	chr1:174993200-174993600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr1:174993200-174993600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:174993200-174995200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:174993200-174998200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:174993200-174998200	Weak transcription	Fetal Intestine Large	intestine
27	chr1:174993200-174998200	Weak transcription	HMEC	breast
28	chr1:174993200-174998400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:174993200-174998400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:174993200-174998600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:174993200-174998600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:174993200-174998600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:174993200-174998600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:174993200-174998800	Weak transcription	Adipose Nuclei	Adipose
35	chr1:174993200-174998800	Weak transcription	Brain Substantia Nigra	brain
36	chr1:174993200-175004800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:174993200-175013800	Weak transcription	Spleen	Spleen

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