Variant report

Variant	rs55918622
Chromosome Location	chr6:11412377-11412378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11386757..11389915-chr6:11410069..11412647,3	MCF-7	breast:
2	chr6:11229922..11234167-chr6:11411662..11415515,7	MCF-7	breast:
3	chr6:11387321..11394874-chr6:11409302..11416244,8	MCF-7	breast:
4	chr6:11231617..11234396-chr6:11409918..11412619,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10947217	0.88[ASN][1000 genomes]
rs12664948	0.89[EUR][1000 genomes]
rs17507230	0.86[ASN][1000 genomes]
rs4074864	0.93[ASN][1000 genomes]
rs4076156	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4301302	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4318876	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713474	0.88[ASN][1000 genomes]
rs4713475	0.88[ASN][1000 genomes]
rs4713478	0.88[ASN][1000 genomes]
rs4713507	0.85[EUR][1000 genomes]
rs56130422	0.81[EUR][1000 genomes]
rs56144403	0.95[ASN][1000 genomes]
rs56155385	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56317766	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59349836	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61650802	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909496	0.87[EUR][1000 genomes]
rs72832932	0.90[ASN][1000 genomes]
rs72832935	0.93[ASN][1000 genomes]
rs72832944	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72832950	0.89[EUR][1000 genomes]
rs73366900	0.95[ASN][1000 genomes]
rs7740502	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11405200-11412400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:11405400-11419400	Weak transcription	Aorta	Aorta
3	chr6:11405800-11412400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:11406000-11412400	Weak transcription	Spleen	Spleen
5	chr6:11406600-11412400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr6:11406600-11414600	Weak transcription	Primary B cells from cord blood	blood
7	chr6:11409600-11412600	Enhancers	HUVEC	blood vessel
8	chr6:11409800-11412600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr6:11410800-11413400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:11410800-11413800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:11411000-11412400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:11411000-11412400	Enhancers	GM12878-XiMat	blood
13	chr6:11411000-11415200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:11411200-11412800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:11411200-11413800	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:11411200-11413800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:11411200-11415000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:11411200-11415000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:11411200-11415600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:11411400-11412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:11411400-11412400	Weak transcription	A549	lung
22	chr6:11411600-11417000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:11411800-11412600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:11412000-11412400	Enhancers	Fetal Kidney	kidney
25	chr6:11412000-11412600	Enhancers	Placenta	Placenta
26	chr6:11412000-11412600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr6:11412000-11412600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr6:11412000-11412600	Enhancers	HepG2	liver
29	chr6:11412000-11412600	Enhancers	NH-A	brain
30	chr6:11412000-11412800	Enhancers	Muscle Satellite Cultured Cells	--
31	chr6:11412000-11412800	Enhancers	HSMM	muscle
32	chr6:11412000-11412800	Enhancers	NHDF-Ad	bronchial
33	chr6:11412000-11413000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:11412000-11413000	Enhancers	Hela-S3	cervix
35	chr6:11412000-11413200	Enhancers	Adipose Nuclei	Adipose
36	chr6:11412000-11414200	Enhancers	Osteobl	bone
37	chr6:11412200-11412600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:11412200-11412600	Enhancers	Brain Cingulate Gyrus	brain
39	chr6:11412200-11412600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr6:11412200-11412600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr6:11412200-11412800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:11412200-11413200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:11412200-11415400	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links