Variant report

Variant	rs4246269
Chromosome Location	chr12:104707562-104707563
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104704742..104707621-chr12:104709723..104711445,2	K562	blood:
2	chr12:104689111..104691925-chr12:104705420..104707657,2	MCF-7	breast:
3	chr12:104706309..104707898-chr12:104718336..104720479,2	K562	blood:
4	chr12:104702286..104704680-chr12:104705294..104708071,2	MCF-7	breast:
5	chr12:104704860..104707713-chr12:104711994..104713971,3	K562	blood:
6	chr12:104688241..104690008-chr12:104706410..104708778,2	MCF-7	breast:
7	chr12:104696110..104698645-chr12:104706800..104709153,2	MCF-7	breast:
8	chr12:104696229..104700878-chr12:104707371..104714338,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000255150	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10735392	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10735393	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs10735395	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10745995	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10745996	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10778311	0.83[JPT][hapmap]
rs10778318	0.83[JPT][hapmap]
rs10778323	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs10861204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11111943	0.89[AMR][1000 genomes]
rs11111955	0.80[CEU][hapmap]
rs11111960	0.83[JPT][hapmap]
rs11111963	0.91[JPT][hapmap]
rs11111983	0.82[AMR][1000 genomes]
rs12426783	0.90[EUR][1000 genomes]
rs17035504	0.86[CEU][hapmap]
rs17202862	0.93[CEU][hapmap]
rs3935021	0.82[EUR][1000 genomes]
rs4129598	0.86[CEU][hapmap]
rs4246264	0.93[CEU][hapmap];0.89[AMR][1000 genomes]
rs4246270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4246271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4388968	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs4447242	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477504	0.80[ASN][1000 genomes]
rs4502051	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4545635	0.93[CEU][hapmap];0.89[AMR][1000 genomes]
rs4614534	0.86[CEU][hapmap]
rs4630362	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4964227	0.93[CEU][hapmap]
rs4964228	0.93[CEU][hapmap]
rs4964257	0.89[AMR][1000 genomes]
rs4964260	0.93[CEU][hapmap];0.89[AMR][1000 genomes]
rs4964288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964627	0.86[CEU][hapmap]
rs4964735	0.83[JPT][hapmap]
rs4964741	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4964752	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964761	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4964779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58129714	0.83[ASN][1000 genomes]
rs6419386	0.89[AMR][1000 genomes]
rs6539137	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6539138	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7132418	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs7138035	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7138317	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7138523	0.83[JPT][hapmap]
rs7139336	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7294997	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7295413	0.81[AMR][1000 genomes]
rs7298613	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7299866	0.86[CEU][hapmap]
rs7301631	0.92[JPT][hapmap]
rs7303483	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7305872	0.82[AMR][1000 genomes]
rs73181916	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73181919	0.91[EUR][1000 genomes]
rs73181926	0.91[EUR][1000 genomes]
rs7342395	0.83[JPT][hapmap]
rs7957725	0.86[CEU][hapmap]
rs7962423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969351	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7969604	0.90[EUR][1000 genomes]
rs7978101	0.82[AMR][1000 genomes]
rs9738614	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9739833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104683800-104723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:104698000-104707600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:104698000-104707800	Weak transcription	Esophagus	oesophagus
4	chr12:104698000-104711400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:104698000-104716200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:104698200-104708400	Genic enhancers	HUVEC	blood vessel
7	chr12:104698200-104708800	Weak transcription	Colonic Mucosa	Colon
8	chr12:104698400-104707800	Weak transcription	Spleen	Spleen
9	chr12:104698400-104716600	Strong transcription	HSMM	muscle
10	chr12:104698400-104718400	Weak transcription	Stomach Mucosa	stomach
11	chr12:104698400-104720600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:104698400-104747600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:104698600-104716200	Strong transcription	NHEK	skin
14	chr12:104699400-104707600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:104699400-104728400	Weak transcription	Fetal Heart	heart
16	chr12:104701000-104724400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:104701400-104707600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:104701600-104709000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:104701600-104733600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:104701800-104707600	Strong transcription	Osteobl	bone
21	chr12:104702000-104716200	Strong transcription	NH-A	brain
22	chr12:104702000-104733600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:104702400-104715600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:104702400-104746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:104702400-104747400	Strong transcription	Dnd41	blood
26	chr12:104702600-104716400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:104703000-104707600	Strong transcription	NHDF-Ad	bronchial
28	chr12:104703000-104707800	Strong transcription	HMEC	breast
29	chr12:104703000-104716400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:104703000-104716600	Strong transcription	Fetal Thymus	thymus
31	chr12:104703000-104716800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr12:104703000-104722400	Strong transcription	K562	blood
33	chr12:104703000-104749200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr12:104703200-104711200	Strong transcription	Primary B cells from cord blood	blood
35	chr12:104703400-104709800	Strong transcription	GM12878-XiMat	blood
36	chr12:104703400-104716800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:104703400-104738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:104703400-104747800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:104703600-104707800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:104703600-104711000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:104703600-104724200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:104703600-104744000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:104703800-104707800	Weak transcription	Gastric	stomach
44	chr12:104703800-104716000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:104703800-104733000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:104704000-104707600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:104704400-104707800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:104704400-104743600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:104704600-104715800	Strong transcription	Left Ventricle	heart
50	chr12:104704600-104716000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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