Variant report

Variant	rs6606748
Chromosome Location	chr12:123952739-123952740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123949352..123951690-chr12:123952165..123954537,2	MCF-7	breast:
2	chr12:123871622..123874415-chr12:123950966..123953833,2	MCF-7	breast:
3	chr12:123950649..123953309-chr12:123967108..123969752,2	K562	blood:
4	chr12:123950525..123953313-chr12:123954953..123957531,2	MCF-7	breast:
5	chr12:123940979..123946241-chr12:123948686..123953480,7	MCF-7	breast:
6	chr12:123945278..123947489-chr12:123951548..123953733,2	K562	blood:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000183955	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11507739	0.90[EUR][1000 genomes]
rs11507740	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13303044	0.81[EUR][1000 genomes]
rs13303080	0.91[EUR][1000 genomes]
rs13303107	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13303167	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13303200	0.91[EUR][1000 genomes]
rs13303266	0.94[EUR][1000 genomes]
rs28413969	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28483351	0.89[EUR][1000 genomes]
rs28497891	0.90[EUR][1000 genomes]
rs28557411	0.89[EUR][1000 genomes]
rs28667043	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34047494	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34351395	0.91[EUR][1000 genomes]
rs34762274	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35090528	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35157218	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35370271	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35970945	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36084544	0.90[EUR][1000 genomes]
rs4047517	0.94[EUR][1000 genomes]
rs56412477	0.97[EUR][1000 genomes]
rs56860279	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71456799	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7297035	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7300562	0.96[EUR][1000 genomes]
rs7306670	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7315901	0.95[EUR][1000 genomes]
rs7960816	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7975122	0.96[EUR][1000 genomes]
rs7978323	0.95[EUR][1000 genomes]
rs9330649	0.87[EUR][1000 genomes]
rs9330650	0.82[EUR][1000 genomes]
rs9697459	0.89[EUR][1000 genomes]
rs9697581	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9697628	0.89[EUR][1000 genomes]
rs9697735	0.89[EUR][1000 genomes]
rs9777736	0.83[EUR][1000 genomes]
rs9778001	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9803116	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123943600-123955800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123943800-123956000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:123943800-123956400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:123943800-123958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:123943800-123959600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:123943800-123959600	Weak transcription	Psoas Muscle	Psoas
7	chr12:123943800-123961200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:123944400-123955800	Weak transcription	NHEK	skin
9	chr12:123944600-123956400	Weak transcription	Stomach Mucosa	stomach
10	chr12:123944600-123995600	Weak transcription	Hela-S3	cervix
11	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
12	chr12:123944800-123964600	Weak transcription	Small Intestine	intestine
13	chr12:123945200-123959200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr12:123945800-123965600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:123946000-123965600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:123946200-123957600	Strong transcription	Fetal Thymus	thymus
17	chr12:123946200-123957800	Strong transcription	Fetal Muscle Leg	muscle
18	chr12:123946400-123953200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr12:123946800-123959200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:123947200-123958600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:123947600-123953600	Strong transcription	Liver	Liver
22	chr12:123947600-123971800	Strong transcription	Fetal Intestine Small	intestine
23	chr12:123947800-123955800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:123948200-123962800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:123949000-123952800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr12:123949000-123953200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:123949000-123953200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:123949000-123953400	Strong transcription	Fetal Intestine Large	intestine
29	chr12:123949000-123957800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:123949000-123966200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:123949000-123984400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:123949200-123953400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:123949200-123955800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:123949200-123957600	Strong transcription	Primary T cells from cord blood	blood
35	chr12:123949200-123957600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:123949600-123956200	Weak transcription	NH-A	brain
37	chr12:123950000-123954400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:123950000-123963200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:123950200-123953200	Weak transcription	HSMM	muscle
40	chr12:123950200-123954600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:123950400-123955800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:123950400-123955800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:123950400-123956000	Weak transcription	Fetal Kidney	kidney
44	chr12:123950400-123956000	Weak transcription	NHDF-Ad	bronchial
45	chr12:123950400-123973000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:123950600-123954200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:123950600-123954600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:123950600-123954600	Weak transcription	Colon Smooth Muscle	Colon
49	chr12:123950600-123955800	Weak transcription	Aorta	Aorta
50	chr12:123950600-123956000	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links