Variant report

Variant	rs6847784
Chromosome Location	chr4:129955832-129955833
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1030830	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10494317	0.85[JPT][hapmap]
rs10518539	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs12500341	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500557	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12503465	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]
rs12504200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512345	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1376202	0.81[YRI][hapmap]
rs17185550	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs172168	1.00[YRI][hapmap]
rs17349255	0.90[JPT][hapmap]
rs17416188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17416706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1756011	0.81[YRI][hapmap]
rs1757938	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1757942	0.81[AFR][1000 genomes]
rs1877836	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1900397	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1993035	0.92[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2044523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2592948	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2597837	0.81[YRI][hapmap]
rs2655311	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs2777823	0.81[AFR][1000 genomes]
rs280601	0.81[YRI][hapmap]
rs3099902	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs36195612	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3980331	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4423892	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4975191	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975293	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55925207	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59540486	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6825433	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs6830023	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6832138	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs6835359	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs6840353	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs6845314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72683669	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72683673	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72683684	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72683693	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685321	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72685324	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685328	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72685351	0.96[ASN][1000 genomes]
rs72685352	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72685353	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72685365	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7654405	0.81[AFR][1000 genomes]
rs7675408	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs796886	0.81[AFR][1000 genomes]
rs921375	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921376	0.98[ASN][1000 genomes]
rs921377	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv966220	chr4:129955209-129958089	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6847784	SCLT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129937200-129964000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:129943200-129960200	Weak transcription	Primary B cells from cord blood	blood
3	chr4:129944400-129961000	Weak transcription	Primary T cells from cord blood	blood
4	chr4:129944600-129962800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr4:129944800-129956000	Weak transcription	Fetal Lung	lung
6	chr4:129944800-129958400	Weak transcription	Liver	Liver
7	chr4:129944800-129965400	Weak transcription	Ovary	ovary
8	chr4:129945600-129958600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:129945600-129981800	Weak transcription	Thymus	Thymus
10	chr4:129951200-129958400	Weak transcription	Dnd41	blood
11	chr4:129951200-129962400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:129951200-129967200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:129951400-129958600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr4:129951400-129976200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:129953400-129962600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:129953600-129965600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:129953600-129965600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:129953800-129958400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:129954200-129959600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr4:129954800-129964400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr4:129955000-129960200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:129955000-129965200	Weak transcription	K562	blood
23	chr4:129955200-129961000	Weak transcription	GM12878-XiMat	blood
24	chr4:129955600-129956400	Weak transcription	Fetal Intestine Large	intestine

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