Variant report

Variant	rs55859780
Chromosome Location	chr2:11500425-11500426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11483149..11486489-chr2:11497401..11501170,3	MCF-7	breast:
2	chr2:11498130..11500885-chr2:11501118..11503134,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10189756	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11890858	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11890982	0.97[ASN][1000 genomes]
rs11891012	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463700	0.95[ASN][1000 genomes]
rs12467795	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12622447	0.93[ASN][1000 genomes]
rs6705170	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6736194	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739310	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743710	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6744083	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6744332	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6759032	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6759164	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6759299	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7589459	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7605784	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7605793	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55859780	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11492600-11500600	Enhancers	Fetal Intestine Large	intestine
2	chr2:11497600-11507400	Weak transcription	Fetal Brain Female	brain
3	chr2:11498000-11504400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:11498200-11502000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:11498200-11505200	Weak transcription	Spleen	Spleen
6	chr2:11498200-11505400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:11498200-11505400	Weak transcription	Liver	Liver
8	chr2:11498200-11505600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:11498200-11507400	Weak transcription	Small Intestine	intestine
10	chr2:11498200-11508000	Weak transcription	Right Atrium	heart
11	chr2:11498800-11505400	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:11498800-11505400	Weak transcription	Placenta	Placenta
13	chr2:11498800-11505600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:11499800-11502800	Weak transcription	A549	lung
15	chr2:11499800-11503000	Weak transcription	Hela-S3	cervix
16	chr2:11500000-11505200	Weak transcription	Fetal Stomach	stomach
17	chr2:11500000-11505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:11500000-11505600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:11500000-11507600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:11500200-11502600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:11500200-11503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:11500200-11505600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:11500200-11507600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:11500400-11500600	Genic enhancers	HepG2	liver
25	chr2:11500400-11503800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:11500400-11507400	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links