Variant report

Variant	rs12189841
Chromosome Location	chr6:26544798-26544799
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26283512..26285254-chr6:26544162..26546329,2	K562	blood:
2	chr6:26214691..26217041-chr6:26543225..26544932,2	K562	blood:
3	chr6:26283470..26285839-chr6:26543063..26545060,2	MCF-7	breast:
4	chr6:26541650..26546578-chr6:26547247..26553909,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187990	Chromatin interaction
ENSG00000158406	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10456328	1.00[CEU][hapmap]
rs10456330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10456332	1.00[AFR][1000 genomes]
rs10484440	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs12194095	0.81[CEU][hapmap]
rs12195971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12199239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12200782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12201802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12201890	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12202419	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12204145	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12205909	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12207181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12207224	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12209651	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12211201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12212145	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12213722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28611089	1.00[AFR][1000 genomes]
rs3757140	0.88[CEU][hapmap]
rs3757145	1.00[CEU][hapmap]
rs3757149	1.00[CEU][hapmap]
rs3800304	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3873182	1.00[AFR][1000 genomes]
rs3927423	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41267923	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4515370	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6456741	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6456742	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6912853	1.00[CHB][hapmap]
rs72843734	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72843802	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72844495	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72844496	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72845509	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs72845515	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7773878	1.00[AFR][1000 genomes]
rs9461246	1.00[CEU][hapmap]
rs9461249	0.81[CEU][hapmap]
rs9467741	0.81[CEU][hapmap]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26539200-26545400	Weak transcription	Gastric	stomach
2	chr6:26539200-26550600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:26539400-26546000	Weak transcription	Ovary	ovary
4	chr6:26539400-26550600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:26539600-26544800	Weak transcription	Psoas Muscle	Psoas
6	chr6:26539600-26544800	Weak transcription	HSMMtube	muscle
7	chr6:26539600-26545200	Weak transcription	Spleen	Spleen
8	chr6:26539600-26545400	Weak transcription	HUVEC	blood vessel
9	chr6:26539600-26549800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:26539600-26550400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:26539600-26550400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:26539600-26550400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:26539600-26550600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:26539600-26553000	Weak transcription	Fetal Heart	heart
15	chr6:26539800-26544800	Weak transcription	Left Ventricle	heart
16	chr6:26539800-26544800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:26539800-26545200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:26539800-26545200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:26539800-26550400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:26539800-26550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:26539800-26550800	Weak transcription	Pancreas	Pancrea
22	chr6:26540000-26544800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:26540000-26545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:26540000-26545400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:26540000-26545400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:26540000-26550800	Weak transcription	Lung	lung
27	chr6:26540200-26545200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:26540200-26545400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:26540200-26550000	Weak transcription	Fetal Kidney	kidney
30	chr6:26540200-26550400	Weak transcription	Colonic Mucosa	Colon
31	chr6:26540400-26544800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:26540400-26544800	Weak transcription	Right Ventricle	heart
33	chr6:26540400-26545000	Weak transcription	Osteobl	bone
34	chr6:26540400-26545200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr6:26540400-26545200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:26540400-26545200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:26540400-26545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:26540400-26545400	Weak transcription	Brain Anterior Caudate	brain
39	chr6:26540400-26545400	Weak transcription	Esophagus	oesophagus
40	chr6:26540400-26545400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:26540400-26545400	Weak transcription	Thymus	Thymus
42	chr6:26540400-26545800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:26540400-26546400	Strong transcription	Adipose Nuclei	Adipose
44	chr6:26540400-26547200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:26540400-26548000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:26540400-26550000	Weak transcription	Stomach Mucosa	stomach
47	chr6:26540400-26550400	Weak transcription	Brain Angular Gyrus	brain
48	chr6:26540400-26550400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:26540400-26550600	Weak transcription	Brain Substantia Nigra	brain
50	chr6:26540600-26544800	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links