Variant report

Variant	rs3753562
Chromosome Location	chr1:174923567-174923568
allele	A/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	FOXA2	chr1:174922792-174923614	A549	lung:	n/a	n/a
2	FOXA1	chr1:174922813-174923610	HepG2	liver:	n/a	n/a
3	FOXA2	chr1:174922756-174923660	HepG2	liver:	n/a	n/a
4	REST	chr1:174922990-174923989	H1-neurons	neurons:	n/a	chr1:174923918-174923931
5	POLR2A	chr1:174923209-174923578	H1-neurons	neurons:	n/a	n/a
6	NFIC	chr1:174921850-174923584	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174923198..174925384-chr1:174966768..174969238,3	K562	blood:
2	chr1:174922181..174924698-chr1:174966768..174969386,2	K562	blood:

Variant related genes	Relation type
ENSG00000229531	TF binding region
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10489332	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11811190	0.80[AFR][1000 genomes]
rs12737503	0.80[AFR][1000 genomes]
rs16847730	0.80[AFR][1000 genomes]
rs41266060	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs41266064	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs41498747	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4565668	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57053120	0.83[AFR][1000 genomes]
rs58618779	0.81[ASN][1000 genomes]
rs59436654	0.87[AFR][1000 genomes]
rs60893569	0.83[AFR][1000 genomes]
rs61028529	0.91[AFR][1000 genomes]
rs6700434	0.91[AFR][1000 genomes];0.85[AMR][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	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1794782	chr1:174900761-174925112	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3753562	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
3	chr1:174908000-174926600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:174908000-174932400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:174908200-174924200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:174908600-174927400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:174908800-174932200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:174910400-174932400	Weak transcription	HSMMtube	muscle
9	chr1:174910800-174925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:174912200-174925400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:174912400-174923800	Weak transcription	Gastric	stomach
13	chr1:174912600-174923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:174912600-174934800	Weak transcription	Left Ventricle	heart
15	chr1:174914800-174932800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:174918600-174923800	Weak transcription	HUVEC	blood vessel
17	chr1:174919200-174926600	Enhancers	Fetal Intestine Large	intestine
18	chr1:174920800-174926200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:174921200-174924400	Enhancers	HepG2	liver
20	chr1:174921200-174924600	Enhancers	Liver	Liver
21	chr1:174921200-174925200	Enhancers	Fetal Intestine Small	intestine
22	chr1:174921400-174925000	Enhancers	Placenta	Placenta
23	chr1:174921800-174924600	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:174921800-174925000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:174922000-174924600	Enhancers	K562	blood
26	chr1:174922000-174925000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:174922200-174923800	Weak transcription	Small Intestine	intestine
28	chr1:174922200-174924000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:174922200-174926600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:174922400-174923800	Enhancers	Primary B cells from cord blood	blood
31	chr1:174922400-174924000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:174922400-174924200	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:174922400-174924400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr1:174922400-174924400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:174922400-174924400	Enhancers	Fetal Lung	lung
36	chr1:174922400-174924800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:174922400-174924800	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:174922400-174925400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:174922600-174923800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr1:174922600-174924000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:174922600-174924400	Enhancers	Brain Anterior Caudate	brain
42	chr1:174922600-174924600	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:174922600-174924600	Enhancers	Brain Substantia Nigra	brain
44	chr1:174922600-174924600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr1:174922600-174924800	Enhancers	Brain Hippocampus Middle	brain
46	chr1:174922600-174925000	Enhancers	Brain Angular Gyrus	brain
47	chr1:174922800-174923800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr1:174922800-174923800	Weak transcription	Stomach Mucosa	stomach
49	chr1:174922800-174924000	Enhancers	Fetal Muscle Leg	muscle
50	chr1:174922800-174925000	Enhancers	Pancreas	Pancrea

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