Variant report

Variant	rs6542781
Chromosome Location	chr2:99083764-99083765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99083098..99084746-chr2:99093436..99095285,2	K562	blood:
2	chr2:99075753..99078697-chr2:99082751..99085272,2	MCF-7	breast:
3	chr2:99066696..99070384-chr2:99081151..99084489,3	K562	blood:
4	chr2:99078388..99081770-chr2:99082152..99084832,3	MCF-7	breast:
5	chr2:99081238..99085183-chr2:99088495..99091939,4	MCF-7	breast:
6	chr2:99080684..99083981-chr2:99090485..99094412,5	MCF-7	breast:
7	chr2:99076723..99078721-chr2:99082880..99084388,2	K562	blood:
8	chr2:99082896..99084437-chr2:99094798..99096441,2	MCF-7	breast:
9	chr2:99074297..99077605-chr2:99081893..99085320,3	MCF-7	breast:
10	chr2:99073761..99075633-chr2:99083363..99085810,2	MCF-7	breast:

No data

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1001856	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10201079	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995531	1.00[YRI][hapmap]
rs2174354	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3754874	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3820947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851143	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6542834	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7559530	1.00[YRI][hapmap]
rs7604208	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007244	chr2:99063753-99136472	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6542781	RPL31	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99072200-99086200	Weak transcription	Fetal Intestine Small	intestine
2	chr2:99072400-99095000	Weak transcription	Fetal Intestine Large	intestine
3	chr2:99072600-99119600	Weak transcription	Aorta	Aorta
4	chr2:99075400-99084000	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:99075600-99091800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:99076200-99083800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:99076400-99095400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:99076600-99085000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:99077600-99085200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:99078400-99084000	Weak transcription	Small Intestine	intestine
11	chr2:99078400-99095600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:99079600-99084000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr2:99079600-99084000	Enhancers	Brain Anterior Caudate	brain
14	chr2:99079600-99084000	Enhancers	Lung	lung
15	chr2:99079600-99084200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:99079800-99084000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr2:99079800-99084000	Enhancers	Left Ventricle	heart
18	chr2:99080000-99083800	Enhancers	Fetal Muscle Leg	muscle
19	chr2:99080000-99084000	Enhancers	Colon Smooth Muscle	Colon
20	chr2:99080200-99094200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:99080400-99083800	Enhancers	Spleen	Spleen
22	chr2:99080400-99084200	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr2:99080400-99091400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:99080800-99084200	Enhancers	Fetal Brain Female	brain
25	chr2:99080800-99084200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr2:99081000-99083800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:99081000-99084400	Enhancers	HSMMtube	muscle
28	chr2:99081200-99084000	Enhancers	Fetal Brain Male	brain
29	chr2:99081400-99095800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:99081600-99084000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:99081600-99084200	Enhancers	HSMM	muscle
32	chr2:99081800-99084200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:99081800-99091400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:99082000-99083800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:99082000-99086800	Weak transcription	Liver	Liver
36	chr2:99082200-99083800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:99082200-99089800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:99082200-99091400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:99082400-99083800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:99082400-99084200	Enhancers	Primary B cells from cord blood	blood
41	chr2:99082400-99084200	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:99082400-99084400	Enhancers	Thymus	Thymus
43	chr2:99082400-99085400	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr2:99082400-99086400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr2:99082400-99088600	Weak transcription	Psoas Muscle	Psoas
46	chr2:99082400-99090200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:99082600-99084000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:99082600-99084200	Enhancers	Fetal Thymus	thymus
49	chr2:99082600-99085600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:99082600-99088200	Weak transcription	Brain Substantia Nigra	brain

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