Variant report

Variant	rs3850839
Chromosome Location	chr1:150234282-150234283
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150233867-150236301	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:150233423-150236363	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:150233848-150236311	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:150233538-150235749	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:150233386-150236861	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:150234272-150234641	U87	brain:	n/a	n/a
7	POLR2A	chr1:150234277-150236293	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFATC1	chr1:150234281-150234998	GM12878	blood:	n/a	n/a
9	MTA3	chr1:150234240-150234608	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:150233468-150237434	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:150233989-150237314	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:150234107-150235266	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:150233438-150234326	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:150233518-150234464	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:150233477-150236279	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:150233483-150236888	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150232349..150234388-chr11:62621868..62623914,2	MCF-7	breast:
2	chr1:150232148..150235043-chr1:150254020..150257209,3	K562	blood:
3	chr1:150206734..150209121-chr1:150233630..150237295,4	MCF-7	breast:

No data

Variant related genes	Relation type
CA14	TF binding region
ENSG00000271845	TF binding region
ENSG00000255717	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000159208	Chromatin interaction
ENSG00000143401	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10888577	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11205347	0.83[CEU][hapmap]
rs11205350	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11205353	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12057558	0.89[ASN][1000 genomes]
rs12121923	0.82[ASN][1000 genomes]
rs12122277	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs12133238	0.82[CEU][hapmap]
rs13374013	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13374483	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2298161	0.84[CHD][hapmap];0.89[GIH][hapmap]
rs3118124	0.84[CEU][hapmap]
rs34908293	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35938158	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3754048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668679	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7535712	0.83[CEU][hapmap]
rs7555995	0.89[CEU][hapmap]

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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv872415	chr1:150210538-150248046	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3850839	MRPS21	cis	cerebellum	SCAN
rs3850839	TNFAIP8L2	cis	cerebellum	SCAN
rs3850839	MRPS21	cis	parietal	SCAN
rs3850839	TARS2	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150229600-150236000	Weak transcription	Lung	lung
2	chr1:150230800-150236000	Weak transcription	Right Ventricle	heart
3	chr1:150230800-150239400	Weak transcription	Fetal Brain Male	brain
4	chr1:150230800-150239400	Weak transcription	Right Atrium	heart
5	chr1:150231200-150235600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:150231800-150237000	Weak transcription	Fetal Brain Female	brain
7	chr1:150232000-150236600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:150232000-150237000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr1:150232200-150237000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:150232200-150237000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:150232400-150235800	Weak transcription	Esophagus	oesophagus
12	chr1:150232400-150236400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:150232400-150237000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:150232600-150235600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:150232600-150235800	Weak transcription	Brain Germinal Matrix	brain
16	chr1:150232600-150235800	Weak transcription	Gastric	stomach
17	chr1:150232600-150236800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:150232600-150237600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:150232600-150240400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:150232800-150234800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:150232800-150234800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:150232800-150236800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:150232800-150236800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:150232800-150236800	Weak transcription	Brain Anterior Caudate	brain
25	chr1:150232800-150236800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:150232800-150237000	Weak transcription	Brain Angular Gyrus	brain
27	chr1:150232800-150237200	Weak transcription	A549	lung
28	chr1:150233000-150234400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:150233000-150234400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:150233000-150234400	Enhancers	Fetal Heart	heart
31	chr1:150233000-150235400	Weak transcription	Fetal Stomach	stomach
32	chr1:150233000-150235400	Enhancers	NHEK	skin
33	chr1:150233000-150235600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:150233000-150235600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:150233000-150235800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:150233000-150235800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:150233000-150235800	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:150233000-150235800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr1:150233000-150236200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:150233000-150236200	Enhancers	Stomach Mucosa	stomach
41	chr1:150233000-150236200	Enhancers	HMEC	breast
42	chr1:150233000-150236600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:150233000-150236600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:150233000-150236600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:150233000-150236800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:150233000-150236800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:150233000-150236800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:150233000-150236800	Weak transcription	Fetal Intestine Large	intestine
49	chr1:150233000-150236800	Weak transcription	Placenta	Placenta
50	chr1:150233000-150236800	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links