Variant report

Variant	rs12196913
Chromosome Location	chr6:24545307-24545308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24539832..24541848-chr6:24544860..24546446,2	MCF-7	breast:
2	chr6:24534085..24537392-chr6:24543907..24547453,3	K562	blood:
3	chr6:24544075..24545945-chr6:24559657..24561591,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10456306	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12199955	0.82[CHB][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs12211030	0.84[ASN][1000 genomes]
rs2817239	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs2817240	0.91[ASN][1000 genomes]
rs2817241	0.91[ASN][1000 genomes]
rs34505453	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34829630	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3903801	0.84[ASW][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62400513	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12196913	GMNN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
2	chr6:24509400-24545800	Weak transcription	Small Intestine	intestine
3	chr6:24535000-24546200	Weak transcription	Pancreas	Pancrea
4	chr6:24535000-24547400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:24535200-24566600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:24535200-24591200	Weak transcription	Fetal Brain Male	brain
7	chr6:24535400-24550000	Weak transcription	Gastric	stomach
8	chr6:24535600-24546000	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:24535600-24546800	Weak transcription	Dnd41	blood
10	chr6:24535600-24547400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:24535600-24560600	Weak transcription	Brain Anterior Caudate	brain
12	chr6:24535600-24560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:24535600-24563200	Weak transcription	Brain Angular Gyrus	brain
14	chr6:24535600-24583400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:24537000-24545400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:24537000-24546200	Weak transcription	Fetal Heart	heart
17	chr6:24538200-24545800	Weak transcription	Aorta	Aorta
18	chr6:24538200-24546000	Weak transcription	HepG2	liver
19	chr6:24538200-24547400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr6:24538400-24547400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr6:24539200-24583200	Weak transcription	Fetal Intestine Small	intestine
22	chr6:24540200-24556200	Weak transcription	Fetal Brain Female	brain
23	chr6:24540800-24546400	Weak transcription	Liver	Liver
24	chr6:24540800-24547400	Weak transcription	Fetal Thymus	thymus
25	chr6:24540800-24547400	Weak transcription	Thymus	Thymus
26	chr6:24540800-24547600	Weak transcription	Fetal Stomach	stomach
27	chr6:24544800-24546200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links