Variant report

Variant	rs12496628
Chromosome Location	chr3:194962593-194962594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194961727..194964469-chr3:194966524..194968567,2	K562	blood:
2	chr3:194960264..194964469-chr3:194965437..194968567,4	K562	blood:
3	chr3:194956680..194958904-chr3:194960408..194963314,3	K562	blood:
4	chr3:194961621..194965085-chr3:194983168..194985887,3	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10933702	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933703	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917438	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918143	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11919965	0.90[EUR][1000 genomes]
rs11921174	0.81[EUR][1000 genomes]
rs11928199	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12485800	0.81[EUR][1000 genomes]
rs12486168	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486220	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486636	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12486835	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488616	0.85[EUR][1000 genomes]
rs12491426	0.85[EUR][1000 genomes]
rs12491902	0.85[EUR][1000 genomes]
rs12492289	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492644	0.90[EUR][1000 genomes]
rs12493888	0.85[EUR][1000 genomes]
rs12494306	0.81[EUR][1000 genomes]
rs12495659	0.85[EUR][1000 genomes]
rs12497444	0.90[EUR][1000 genomes]
rs12497906	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12498063	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35899174	0.90[EUR][1000 genomes]
rs56281422	0.90[EUR][1000 genomes]
rs56835677	0.85[EUR][1000 genomes]
rs58113840	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59579668	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60677730	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61022222	0.85[EUR][1000 genomes]
rs6437466	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66510151	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67388686	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67413252	0.86[EUR][1000 genomes]
rs67484513	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777904	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6785108	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790425	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6804467	0.90[EUR][1000 genomes]
rs72499624	0.85[EUR][1000 genomes]
rs73069019	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7642127	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999331	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
13	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
15	nsv984539	chr3:194945800-194984579	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194945400-194971600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:194946000-194971400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:194955000-194973200	Weak transcription	NH-A	brain
4	chr3:194956400-194966800	Weak transcription	HSMM	muscle
5	chr3:194956600-194972800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:194957200-194971800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:194957200-194972800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:194957400-194979800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:194957600-194975400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:194958000-194966600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:194958200-194964000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:194958200-194964600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:194958200-194966200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:194958200-194966200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:194958200-194966400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:194958200-194967000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:194958200-194967000	Weak transcription	Dnd41	blood
18	chr3:194958200-194967600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:194958400-194966200	Weak transcription	HepG2	liver
20	chr3:194958400-194979400	Weak transcription	K562	blood
21	chr3:194958600-194970200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:194958800-194964000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:194958800-194971600	Weak transcription	Thymus	Thymus
24	chr3:194959200-194968000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:194959200-194979600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:194959600-194966200	Weak transcription	Fetal Intestine Small	intestine
27	chr3:194959600-194971600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:194959600-194971600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:194959600-194973200	Weak transcription	Osteobl	bone
30	chr3:194959800-194962600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:194959800-194962800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr3:194959800-194962800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:194959800-194963000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:194959800-194966200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:194959800-194966200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:194959800-194971400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:194959800-194971600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:194959800-194971600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:194959800-194971600	Weak transcription	Placenta	Placenta
40	chr3:194959800-194973400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:194959800-194973800	Weak transcription	NHLF	lung
42	chr3:194960000-194968600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:194960000-194978600	Weak transcription	Brain Substantia Nigra	brain
44	chr3:194960200-194967800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:194960200-194971400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:194960200-194973400	Weak transcription	Fetal Intestine Large	intestine
47	chr3:194960400-194967200	Weak transcription	Primary T cells from cord blood	blood
48	chr3:194961000-194962600	Enhancers	Esophagus	oesophagus
49	chr3:194961200-194962600	Genic enhancers	Fetal Stomach	stomach
50	chr3:194961200-194966200	Weak transcription	Fetal Lung	lung

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