Variant report

Variant	rs17052424
Chromosome Location	chr3:52802168-52802169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52800007..52802785-chr3:52803271..52804893,2	K562	blood:
2	chr3:52799929..52802463-chr3:52808466..52811160,2	K562	blood:

Variant related genes	Relation type
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1344932	1.00[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17052322	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17052355	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17052427	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs1971811	0.85[AFR][1000 genomes]
rs2079928	1.00[AMR][1000 genomes]
rs2336161	1.00[MEX][hapmap]
rs41415947	0.80[ASW][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs56815357	0.83[AFR][1000 genomes]
rs57401769	0.85[AFR][1000 genomes]
rs57522359	1.00[AMR][1000 genomes]
rs57607481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57787182	0.84[AFR][1000 genomes]
rs57931767	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58057636	1.00[AMR][1000 genomes]
rs59182119	1.00[AMR][1000 genomes]
rs60133283	1.00[AMR][1000 genomes]
rs60351358	0.91[AFR][1000 genomes]
rs60945641	1.00[AMR][1000 genomes]
rs61229218	0.83[AMR][1000 genomes]
rs6767229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6778100	1.00[MEX][hapmap]
rs6779626	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6796577	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6803865	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6809065	0.85[AFR][1000 genomes]
rs72960288	0.82[AFR][1000 genomes]
rs72960294	0.84[AFR][1000 genomes]
rs72960298	1.00[AMR][1000 genomes]
rs7615320	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7616059	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7644379	1.00[MEX][hapmap]
rs7649820	0.91[AFR][1000 genomes];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	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17052424	SPCS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
7	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:52768000-52803600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:52768800-52803000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:52774000-52803400	Weak transcription	K562	blood
12	chr3:52775200-52802600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:52775800-52802800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52775800-52802800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:52778400-52802400	Strong transcription	Liver	Liver
16	chr3:52783200-52803800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:52784800-52804000	Weak transcription	Aorta	Aorta
18	chr3:52786200-52803600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:52786400-52803600	Weak transcription	Stomach Mucosa	stomach
20	chr3:52786400-52803800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:52786600-52802600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:52786800-52802600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:52786800-52802600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:52787600-52803600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:52787600-52803600	Weak transcription	Colonic Mucosa	Colon
26	chr3:52787800-52803600	Weak transcription	Gastric	stomach
27	chr3:52787800-52804000	Weak transcription	Right Ventricle	heart
28	chr3:52788200-52802600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:52788200-52803000	Weak transcription	Pancreas	Pancrea
30	chr3:52788200-52803600	Weak transcription	Esophagus	oesophagus
31	chr3:52790200-52802800	Strong transcription	Placenta	Placenta
32	chr3:52790600-52802600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:52790600-52802600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:52790800-52802600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:52791000-52802600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:52791000-52802800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:52791000-52803200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:52791200-52802600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:52791400-52804000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr3:52792600-52802600	Strong transcription	Fetal Brain Female	brain
41	chr3:52792800-52802400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:52792800-52802600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:52792800-52802600	Strong transcription	Fetal Muscle Leg	muscle
44	chr3:52794200-52803600	Weak transcription	Ovary	ovary
45	chr3:52794200-52803600	Weak transcription	Thymus	Thymus
46	chr3:52794200-52803800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:52794800-52802600	Strong transcription	Fetal Intestine Large	intestine
48	chr3:52795200-52803400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:52796600-52802800	Strong transcription	Fetal Intestine Small	intestine
50	chr3:52797400-52802400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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