Variant report

Variant	rs17337491
Chromosome Location	chr4:129254598-129254599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129246798..129250551-chr4:129252824..129254939,4	K562	blood:
2	chr4:129209081..129210870-chr4:129253723..129256710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164040	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12499030	0.86[AFR][1000 genomes]
rs12508205	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12645655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062456	1.00[ASW][hapmap]
rs2133465	1.00[ASW][hapmap]
rs4305531	1.00[ASW][hapmap]
rs4362840	1.00[ASW][hapmap]
rs4975182	1.00[CHB][hapmap]
rs4975221	1.00[ASW][hapmap]
rs55938082	0.82[AMR][1000 genomes]
rs6534679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6822446	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6840580	1.00[ASW][hapmap]
rs7441245	1.00[ASW][hapmap]

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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17337491	SGCE	trans	lymphoblastoid	seeQTL
rs17337491	ZSCAN2	trans	lymphoblastoid	RTeQTL
rs17337491	HSPA4L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129222200-129264200	Weak transcription	Fetal Thymus	thymus
2	chr4:129231800-129255000	Weak transcription	Left Ventricle	heart
3	chr4:129231800-129261000	Weak transcription	Adipose Nuclei	Adipose
4	chr4:129242600-129254800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:129244800-129259200	Weak transcription	Stomach Mucosa	stomach
6	chr4:129245000-129259200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:129245200-129259200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:129245200-129259200	Weak transcription	A549	lung
9	chr4:129245600-129260000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:129245600-129263400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:129249600-129254600	Weak transcription	K562	blood
12	chr4:129249600-129259200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:129251400-129279600	Weak transcription	Primary T cells from cord blood	blood
14	chr4:129251600-129255400	Enhancers	Fetal Heart	heart
15	chr4:129253400-129255000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:129254000-129259000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:129254000-129259000	Weak transcription	Osteobl	bone
18	chr4:129254000-129259200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:129254000-129259200	Weak transcription	HSMMtube	muscle
20	chr4:129254000-129259200	Weak transcription	NH-A	brain
21	chr4:129254400-129254600	Weak transcription	HSMM	muscle

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