Variant report

Variant	rs12749957
Chromosome Location	chr1:246911337-246911338
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246911249..246913997-chr1:246914503..246916490,2	K562	blood:
2	chr1:246867885..246870245-chr1:246910384..246912809,2	MCF-7	breast:
3	chr1:246886275..246889143-chr1:246911120..246913975,3	MCF-7	breast:
4	chr1:246887255..246889228-chr1:246910662..246914076,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10924825	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11807753	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12075623	0.83[ASN][1000 genomes]
rs34631393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35805720	0.81[ASN][1000 genomes]
rs3795467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3924455	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41308152	0.81[ASN][1000 genomes]
rs61852474	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61852478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61852484	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61852516	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61855376	0.82[AMR][1000 genomes]
rs6657743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6667792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6693529	0.82[ASN][1000 genomes]
rs6694274	1.00[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7410903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7518952	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7527938	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv870294	chr1:246877043-246927940	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
4	chr1:246890200-246913200	Strong transcription	Fetal Muscle Leg	muscle
5	chr1:246890600-246914000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:246891800-246911600	Strong transcription	Liver	Liver
7	chr1:246892400-246912000	Strong transcription	Dnd41	blood
8	chr1:246892600-246924400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:246893800-246912800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:246894600-246923800	Weak transcription	Pancreas	Pancrea
11	chr1:246895000-246912000	Weak transcription	Spleen	Spleen
12	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
14	chr1:246896400-246917000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:246897600-246912400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:246900000-246917600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:246900800-246912200	Weak transcription	Esophagus	oesophagus
18	chr1:246901200-246924000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:246902600-246912200	Weak transcription	Lung	lung
20	chr1:246902800-246923200	Weak transcription	Fetal Brain Male	brain
21	chr1:246902800-246923800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:246903000-246917200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:246904400-246911400	Weak transcription	Fetal Lung	lung
25	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:246905000-246911600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:246905000-246922200	Weak transcription	Brain Germinal Matrix	brain
28	chr1:246905000-246922200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:246905000-246923600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:246905000-246923800	Weak transcription	Thymus	Thymus
31	chr1:246905000-246924000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
33	chr1:246905600-246923400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:246905600-246923800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:246905800-246912000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:246905800-246923800	Weak transcription	Colonic Mucosa	Colon
37	chr1:246905800-246931600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:246906000-246923800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:246906200-246917200	Weak transcription	GM12878-XiMat	blood
40	chr1:246906600-246911400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:246906600-246914000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:246906800-246911400	Weak transcription	Fetal Intestine Small	intestine
43	chr1:246906800-246923000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:246906800-246923800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:246907000-246923600	Weak transcription	Aorta	Aorta
46	chr1:246907400-246922200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:246908000-246913600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:246908600-246911400	Weak transcription	Gastric	stomach
49	chr1:246908600-246911400	Weak transcription	Ovary	ovary
50	chr1:246908600-246923400	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links