Variant report

Variant	rs6542834
Chromosome Location	chr2:99221939-99221940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:99221574-99222161	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:99221936-99221988	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr2:99220954-99222302	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:99221480-99222065	HepG2	liver:	n/a	n/a
5	MXI1	chr2:99220750-99221951	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr2:99221063-99222045	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:99220917-99222056	GM12891	blood:	n/a	n/a
8	POLR2A	chr2:99221082-99222457	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:99220955-99222017	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr2:99220912-99222185	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:99221594-99221946	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99220491..99222361-chr2:99223823..99225591,2	MCF-7	breast:
2	chr2:99221557..99223102-chr2:99346482..99348239,2	MCF-7	breast:
3	chr2:99221188..99224105-chr2:99225000..99227009,2	K562	blood:

Variant related genes	Relation type
UNC50	TF binding region
COA5	TF binding region
ENSG00000115446	Chromatin interaction
ENSG00000071073	Chromatin interaction
ENSG00000183513	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1001856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201079	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];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2174354	0.86[EUR][1000 genomes]
rs3754874	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3820947	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851143	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542781	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7604208	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv1013941	chr2:99116255-99317933	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535834	chr2:99116255-99317933	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6542834	RPL31	cis	cerebellum	SCAN
rs6542834	SNRNP200	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99169400-99222600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:99199600-99223400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:99201800-99223000	Weak transcription	Stomach Mucosa	stomach
4	chr2:99203000-99222800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:99210800-99223200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:99212200-99222800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:99212600-99223600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:99213000-99222400	Strong transcription	Primary B cells from cord blood	blood
9	chr2:99213000-99222600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr2:99213000-99223000	Strong transcription	Fetal Thymus	thymus
11	chr2:99213200-99223600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:99214200-99223000	Weak transcription	Fetal Brain Male	brain
13	chr2:99214400-99222600	Weak transcription	Brain Angular Gyrus	brain
14	chr2:99214800-99222600	Strong transcription	Primary hematopoietic stem cells	blood
15	chr2:99216800-99222400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:99216800-99223600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:99217000-99223400	Weak transcription	A549	lung
18	chr2:99217000-99223600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:99217200-99223600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:99217200-99223600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:99217400-99223000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:99217400-99223000	Weak transcription	Osteobl	bone
23	chr2:99217400-99223600	Weak transcription	NH-A	brain
24	chr2:99217600-99222400	Weak transcription	Small Intestine	intestine
25	chr2:99217600-99222600	Weak transcription	Brain Germinal Matrix	brain
26	chr2:99218400-99222400	Weak transcription	Aorta	Aorta
27	chr2:99218400-99222600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:99218400-99222600	Weak transcription	Gastric	stomach
29	chr2:99218400-99222600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:99218400-99222600	Weak transcription	Spleen	Spleen
31	chr2:99218400-99222800	Weak transcription	Esophagus	oesophagus
32	chr2:99218400-99222800	Weak transcription	Pancreas	Pancrea
33	chr2:99218400-99223400	Weak transcription	NHLF	lung
34	chr2:99218600-99223000	Weak transcription	Ovary	ovary
35	chr2:99218600-99223400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:99218800-99222800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:99218800-99222800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:99218800-99222800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:99218800-99222800	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:99219000-99222600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:99219000-99222800	Weak transcription	Right Ventricle	heart
42	chr2:99219000-99223000	Weak transcription	Fetal Stomach	stomach
43	chr2:99219200-99223000	Weak transcription	Fetal Intestine Small	intestine
44	chr2:99219400-99223000	Weak transcription	GM12878-XiMat	blood
45	chr2:99219600-99222200	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:99219600-99222600	Weak transcription	Brain Substantia Nigra	brain
47	chr2:99219600-99223000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:99219600-99223000	Weak transcription	Fetal Brain Female	brain
49	chr2:99219600-99223200	Weak transcription	Colonic Mucosa	Colon
50	chr2:99219600-99223600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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