Variant report

Variant	rs12503465
Chromosome Location	chr4:129925388-129925389
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:129918148..129920594-chr4:129924035..129926675,2	K562	blood:
2	chr4:129919094..129920682-chr4:129924284..129926675,2	K562	blood:

Variant related genes	Relation type
ENSG00000151466	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1030830	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494317	0.89[JPT][hapmap]
rs10518539	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs12500341	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12500557	0.80[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12504200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12512345	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17185550	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs172168	0.93[YRI][hapmap]
rs17349255	0.88[JPT][hapmap]
rs17416188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17416706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1757938	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1757942	0.81[AFR][1000 genomes]
rs1877836	0.89[JPT][hapmap]
rs1900397	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1993035	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs2044523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2592948	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs2655311	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs2777823	0.81[AFR][1000 genomes]
rs3099902	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs36195612	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3980331	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4423892	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs4975191	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4975293	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55925207	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59540486	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6825433	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs6830023	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6832138	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs6835359	0.87[CEU][hapmap];0.88[JPT][hapmap]
rs6840353	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs6845314	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6847784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72683669	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72683673	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72683684	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72683693	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72685321	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685324	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72685328	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72685351	0.94[ASN][1000 genomes]
rs72685352	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72685353	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72685365	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7654405	0.81[AFR][1000 genomes]
rs7675408	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs796886	0.81[AFR][1000 genomes]
rs921375	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921376	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921377	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
2	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1026938	chr4:129770961-129936205	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1030513	chr4:129770961-129965026	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv870175	chr4:129771718-129937945	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1026772	chr4:129773881-129936205	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv461638	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv595398	chr4:129774375-129927804	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1018994	chr4:129775612-129933968	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1026722	chr4:129801602-129929219	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv537252	chr4:129801602-129929219	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12503465	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129868200-129935600	Weak transcription	HSMM	muscle
2	chr4:129878400-129925600	Weak transcription	HSMMtube	muscle
3	chr4:129906200-129935800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:129908200-129927000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:129911400-129936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:129917200-129926000	Weak transcription	Ovary	ovary
7	chr4:129917400-129927200	Weak transcription	Primary B cells from cord blood	blood
8	chr4:129917400-129935800	Weak transcription	Pancreas	Pancrea
9	chr4:129917400-129936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:129917400-129936200	Weak transcription	Left Ventricle	heart
11	chr4:129917400-129942400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:129917600-129926800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:129920200-129926000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:129920600-129926800	Weak transcription	NHDF-Ad	bronchial
15	chr4:129920600-129927600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr4:129920600-129936000	Weak transcription	Fetal Thymus	thymus
17	chr4:129920800-129927000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr4:129924800-129927200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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