Variant report

Variant	rs17052427
Chromosome Location	chr3:52809996-52809997
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	CEBPB	chr3:52809966-52810321	HepG2	liver:	n/a	n/a
2	HEY1	chr3:52809155-52810388	HepG2	liver:	n/a	n/a
3	MAZ	chr3:52809409-52810100	HepG2	liver:	n/a	chr3:52809645-52809655
4	POLR2A	chr3:52809971-52810334	HepG2	liver:	n/a	n/a
5	RCOR1	chr3:52809322-52810142	HepG2	liver:	n/a	n/a
6	MYBL2	chr3:52808979-52810238	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:52809204-52810353	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:52809398-52809996	HepG2	liver:	n/a	n/a
9	SMC3	chr3:52809327-52810020	HepG2	liver:	n/a	n/a
10	NFIC	chr3:52809153-52810071	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52799929..52802463-chr3:52808466..52811160,2	K562	blood:

Variant related genes	Relation type
ITIH1	TF binding region

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1344932	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs17052322	1.00[MEX][hapmap]
rs17052355	1.00[MEX][hapmap]
rs17052424	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2079928	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336161	1.00[MEX][hapmap]
rs57522359	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57607481	1.00[AMR][1000 genomes]
rs57789542	0.90[AFR][1000 genomes]
rs57931767	1.00[AMR][1000 genomes]
rs58057636	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59182119	1.00[AMR][1000 genomes]
rs60133283	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60945641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61229218	0.83[AMR][1000 genomes]
rs6767229	1.00[AMR][1000 genomes]
rs6778100	1.00[MEX][hapmap]
rs6779626	1.00[AMR][1000 genomes]
rs6796577	1.00[AMR][1000 genomes]
rs6803865	1.00[AMR][1000 genomes]
rs72960298	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7615320	1.00[AMR][1000 genomes]
rs7616059	1.00[AMR][1000 genomes]
rs7644379	1.00[MEX][hapmap]
rs7649820	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17052427	SPCS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52805600-52825800	Weak transcription	Right Ventricle	heart
2	chr3:52805800-52810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:52805800-52812000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:52806000-52810000	Weak transcription	Pancreas	Pancrea
5	chr3:52806000-52811600	Weak transcription	Adipose Nuclei	Adipose
6	chr3:52806800-52810400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:52808600-52810800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:52808600-52811200	Enhancers	Fetal Intestine Large	intestine
9	chr3:52808600-52812000	Enhancers	Fetal Intestine Small	intestine
10	chr3:52808800-52810200	Flanking Active TSS	HepG2	liver
11	chr3:52808800-52810600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr3:52809000-52810200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:52809000-52811400	Enhancers	Stomach Mucosa	stomach
14	chr3:52809200-52810000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:52809200-52810200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr3:52809200-52810200	Enhancers	Fetal Heart	heart
17	chr3:52809200-52810800	Enhancers	Fetal Thymus	thymus
18	chr3:52809400-52810400	Enhancers	K562	blood
19	chr3:52809600-52810000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:52809600-52810400	Enhancers	Thymus	Thymus
21	chr3:52809800-52811000	Flanking Active TSS	Liver	Liver

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