Variant report

Variant	rs6779870
Chromosome Location	chr3:140958061-140958062
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	chr3:140954329..140957093-chr3:140957221..140960303,3	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1026716	0.80[TSI][hapmap]
rs10935425	0.82[MEX][hapmap]
rs10935427	0.83[MEX][hapmap];0.82[TSI][hapmap]
rs12486843	0.81[EUR][1000 genomes]
rs13069904	0.92[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs1511371	0.89[EUR][1000 genomes]
rs1511372	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1511373	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1877222	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1877223	0.87[MEX][hapmap]
rs2048459	0.91[EUR][1000 genomes]
rs2137016	0.83[MEX][hapmap]
rs2291039	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683585	0.91[EUR][1000 genomes]
rs4683586	0.92[CEU][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs6439988	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7613113	0.88[EUR][1000 genomes]
rs7652530	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs967526	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs9875630	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6779870	XRN1	cis	parietal	SCAN
rs6779870	ACPL2	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140959000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:140951800-140958800	Weak transcription	Osteobl	bone
4	chr3:140951800-140959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:140951800-140960200	Weak transcription	Esophagus	oesophagus
6	chr3:140951800-140960400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:140951800-140962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:140951800-140962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:140952000-140958400	Weak transcription	Fetal Kidney	kidney
10	chr3:140952000-140959000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:140952000-140959000	Weak transcription	Placenta	Placenta
12	chr3:140952000-140959600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:140952000-140962000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr3:140952400-140959600	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:140953000-140958800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:140953200-140959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:140953400-140958800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:140953600-140959600	Genic enhancers	Fetal Thymus	thymus
19	chr3:140953600-140960200	Weak transcription	Spleen	Spleen
20	chr3:140953800-140958400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:140954000-140959200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:140954200-140959200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:140954800-140958600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:140955000-140959400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:140955000-140959600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:140955000-140960200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:140955000-140960600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:140955000-140961800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:140955200-140958200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:140955200-140958200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:140955200-140959000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:140955200-140962000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:140955400-140959000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:140955400-140968400	Genic enhancers	Dnd41	blood
36	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:140955600-140959800	Weak transcription	Fetal Intestine Large	intestine
38	chr3:140956000-140959400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr3:140956200-140962600	Enhancers	Fetal Brain Male	brain
40	chr3:140956400-140958200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:140956400-140958400	Weak transcription	HepG2	liver
42	chr3:140956400-140959200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:140956400-140959800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr3:140956400-140960400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:140956400-140962600	Genic enhancers	Thymus	Thymus
46	chr3:140956600-140958200	Weak transcription	Brain Angular Gyrus	brain
47	chr3:140956600-140960000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:140956600-140962600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr3:140956600-140962600	Enhancers	Fetal Muscle Leg	muscle
50	chr3:140956600-140962600	Enhancers	Left Ventricle	heart

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