Variant report

Variant	rs9307530
Chromosome Location	chr4:124585951-124585952
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	chr4:124584154..124586562-chr4:124589727..124591476,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRY1-2	chr4:124582908-124587987	ENSG00000249464
2	lnc-SPRY1-2	chr4:124582908-124589223	NONHSAT098196

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10006717	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10011376	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10518422	0.85[EUR][1000 genomes]
rs11728834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736969	0.85[EUR][1000 genomes]
rs12499994	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12508844	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509035	0.85[EUR][1000 genomes]
rs12509315	0.87[EUR][1000 genomes]
rs13115374	0.88[EUR][1000 genomes]
rs13129658	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541733	0.90[ASN][1000 genomes]
rs2553359	0.91[ASN][1000 genomes]
rs2589843	0.85[ASN][1000 genomes]
rs2589847	0.91[ASN][1000 genomes]
rs35117841	0.85[EUR][1000 genomes]
rs6534420	0.91[ASN][1000 genomes]
rs7660796	0.84[EUR][1000 genomes]
rs9996214	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999581	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv469710	chr4:124474286-124623722	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv482747	chr4:124474286-124623722	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830047	chr4:124504051-124699142	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv879873	chr4:124528452-124590869	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv879874	chr4:124550693-124607201	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3496592	chr4:124582304-124586904	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3496593	chr4:124582304-124586904	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9307530	TMEM155	cis	cerebellum	SCAN
rs9307530	KIAA1109	cis	cerebellum	SCAN
rs9307530	BBS12	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124573000-124586400	Weak transcription	Pancreas	Pancrea
2	chr4:124573000-124598200	Weak transcription	Right Atrium	heart
3	chr4:124573400-124592400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:124573800-124595200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:124577800-124594000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:124578200-124593000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:124578200-124596600	Weak transcription	Aorta	Aorta
8	chr4:124580800-124605000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:124581400-124587000	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:124582400-124587600	Weak transcription	Fetal Intestine Small	intestine
11	chr4:124582400-124587600	Weak transcription	HepG2	liver
12	chr4:124582400-124594000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:124582800-124586600	Weak transcription	Fetal Intestine Large	intestine
14	chr4:124584400-124596000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:124585400-124592800	Weak transcription	Psoas Muscle	Psoas
16	chr4:124585400-124597800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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