Variant report

Variant	rs12246543
Chromosome Location	chr10:93301428-93301429
allele	C/G
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	FOXP2	chr10:93301087-93301694	SK-N-MC	brain:	n/a	n/a
2	TCF7L2	chr10:93300324-93302257	Hela-S3	cervix:	n/a	chr10:93301734-93301741 chr10:93301494-93301508
3	EP300	chr10:93301378-93301636	Hela-S3	cervix:	n/a	n/a
4	RCOR1	chr10:93300414-93301594	Hela-S3	cervix:	n/a	n/a
5	MAX	chr10:93301295-93301670	Hela-S3	cervix:	n/a	chr10:93301389-93301398 chr10:93301623-93301631
6	ELK4	chr10:93301200-93301639	Hela-S3	cervix:	n/a	chr10:93301418-93301429
7	POLR2A	chr10:93301062-93301684	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr10:93300559-93301932	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr10:93301284-93301642	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:93300705..93303047-chr10:93391078..93393805,2	MCF-7	breast:
2	chr10:93297416..93300148-chr10:93300750..93302259,2	MCF-7	breast:

Variant related genes	Relation type
RPS27P1	TF binding region
ENSG00000119938	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10881918	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881919	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881923	0.81[ASN][1000 genomes]
rs11186608	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11186610	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186611	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11186613	0.81[ASN][1000 genomes]
rs12241797	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12246270	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12255223	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256369	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12256726	0.81[ASN][1000 genomes]
rs12260868	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12260905	0.81[ASN][1000 genomes]
rs12263117	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs12268133	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs1411120	0.81[ASN][1000 genomes]
rs1411121	0.81[ASN][1000 genomes]
rs17106760	0.81[ASN][1000 genomes]
rs2094710	0.81[ASN][1000 genomes]
rs4933659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933660	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933661	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933662	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933663	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4933665	0.81[ASN][1000 genomes]
rs4933666	0.81[ASN][1000 genomes]
rs4933667	0.81[ASN][1000 genomes]
rs4933668	0.81[ASN][1000 genomes]
rs4933669	0.81[ASN][1000 genomes]
rs55753810	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55785441	0.86[EUR][1000 genomes]
rs56007503	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56198147	0.81[ASN][1000 genomes]
rs59997744	0.81[ASN][1000 genomes]
rs7068979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074115	0.81[ASN][1000 genomes]
rs716361	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs72819225	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72819249	0.81[ASN][1000 genomes]
rs72819252	0.81[ASN][1000 genomes]
rs7477129	0.81[ASN][1000 genomes]
rs7895083	0.81[ASN][1000 genomes]
rs7908831	0.81[ASN][1000 genomes]
rs7910891	1.00[CHB][hapmap]
rs928118	0.81[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12246543	MARCH5	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93296200-93312200	Weak transcription	Psoas Muscle	Psoas
2	chr10:93296600-93302000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr10:93297000-93311400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:93297000-93311400	Weak transcription	Left Ventricle	heart
5	chr10:93297200-93302000	Weak transcription	Fetal Kidney	kidney
6	chr10:93297600-93301800	Weak transcription	Ovary	ovary
7	chr10:93299400-93311400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr10:93300000-93302800	Enhancers	Hela-S3	cervix
9	chr10:93300000-93304200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:93300000-93306600	Enhancers	Fetal Lung	lung
11	chr10:93300200-93302200	Enhancers	GM12878-XiMat	blood
12	chr10:93300400-93301600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr10:93300400-93302200	Enhancers	Fetal Stomach	stomach
14	chr10:93300800-93301600	Enhancers	Dnd41	blood
15	chr10:93300800-93302600	Enhancers	Fetal Brain Male	brain
16	chr10:93300800-93302600	Enhancers	NHLF	lung
17	chr10:93300800-93302800	Enhancers	Fetal Muscle Trunk	muscle
18	chr10:93301000-93302600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:93301000-93302800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:93301000-93314800	Weak transcription	Aorta	Aorta
21	chr10:93301200-93301600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:93301200-93301600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr10:93301200-93301600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:93301200-93301600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr10:93301200-93301600	Enhancers	Osteobl	bone
26	chr10:93301200-93302000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr10:93301200-93302600	Enhancers	Fetal Muscle Leg	muscle
28	chr10:93301400-93301800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:93301400-93301800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr10:93301400-93302600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links