Variant report

Variant	rs1044927
Chromosome Location	chr7:140702682-140702683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:140701817-140703904	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:140701133..140705248-chr7:140712773..140716152,4	K562	blood:
2	chr7:140701510..140704472-chr7:140705422..140707944,2	MCF-7	breast:
3	chr7:140700885..140703018-chr7:140705505..140708464,2	MCF-7	breast:
4	chr7:140700390..140704443-chr7:140712773..140714840,3	K562	blood:
5	chr7:140702442..140704379-chr7:140707606..140710163,3	K562	blood:
6	chr7:140701629..140704089-chr7:140709964..140711981,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BRAF-2	chr7:140702410-140704649	ENSG00000273081.1

No data

Variant related genes	Relation type
CCT4P1	TF binding region
ENSG00000090263	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10215245	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10255167	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10265001	0.81[EUR][1000 genomes]
rs10268118	0.86[EUR][1000 genomes]
rs1089264	0.88[ASN][1000 genomes]
rs10952364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12538296	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12703284	0.80[ASN][1000 genomes]
rs13234490	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13236223	0.82[EUR][1000 genomes]
rs13236704	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1476816	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1860720	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1961288	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2079827	0.86[ASN][1000 genomes]
rs2079978	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs246739	0.86[ASN][1000 genomes]
rs2688430	0.88[ASN][1000 genomes]
rs3805116	1.00[CHB][hapmap]
rs3852286	0.87[EUR][1000 genomes]
rs3864527	0.87[EUR][1000 genomes]
rs38715	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs38717	0.84[ASN][1000 genomes]
rs38718	0.82[ASN][1000 genomes]
rs38720	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs38722	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs38723	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs38726	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs38730	0.95[ASN][1000 genomes]
rs38731	0.95[ASN][1000 genomes]
rs38734	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs38736	0.93[ASN][1000 genomes]
rs38739	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs38740	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs4726196	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4726225	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs488795	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs490810	0.80[ASN][1000 genomes]
rs512177	0.80[ASN][1000 genomes]
rs512509	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs528957	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs533441	0.80[ASN][1000 genomes]
rs544081	0.82[ASN][1000 genomes]
rs545121	0.80[ASN][1000 genomes]
rs557962	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs569584	0.82[ASN][1000 genomes]
rs579518	0.80[ASN][1000 genomes]
rs58901822	0.86[ASN][1000 genomes]
rs62485452	0.82[ASN][1000 genomes]
rs62485453	0.86[ASN][1000 genomes]
rs6464217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464260	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6464284	0.80[ASN][1000 genomes]
rs6662	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6967214	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6971577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7792447	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7801518	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801117	0.88[ASN][1000 genomes]
rs801121	0.88[ASN][1000 genomes]
rs801127	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs801155	0.82[ASN][1000 genomes]
rs801159	0.80[ASN][1000 genomes]
rs9274	1.00[CHB][hapmap]

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	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1044927	MRPS33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140698400-140705400	Weak transcription	Fetal Lung	lung
2	chr7:140698600-140713000	Weak transcription	Psoas Muscle	Psoas
3	chr7:140699000-140704000	Enhancers	Fetal Intestine Large	intestine
4	chr7:140699400-140703800	Enhancers	Fetal Intestine Small	intestine
5	chr7:140699600-140713800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:140700400-140703800	Enhancers	Liver	Liver
7	chr7:140700600-140705600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr7:140700800-140703000	Enhancers	Duodenum Mucosa	Duodenum
9	chr7:140700800-140703800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr7:140701000-140706600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:140701200-140703200	Weak transcription	Pancreas	Pancrea
12	chr7:140701200-140705600	Weak transcription	Small Intestine	intestine
13	chr7:140701400-140713400	Weak transcription	NHLF	lung
14	chr7:140701600-140702800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:140702000-140704800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr7:140702000-140705200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:140702000-140705400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:140702000-140705400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr7:140702000-140707400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:140702000-140709200	Weak transcription	Fetal Kidney	kidney
21	chr7:140702200-140705200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:140702200-140705400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:140702200-140705600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:140702400-140705400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:140702400-140705600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr7:140702600-140703800	Flanking Active TSS	HepG2	liver
27	chr7:140702600-140705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links