Variant report

Variant	rs12409561
Chromosome Location	chr1:78440469-78440470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:78439971-78440471	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:78440196-78440512	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:78440219-78441189	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:78440121-78441061	HepG2	liver:	n/a	n/a
5	EBF1	chr1:78440446-78440710	GM12878	blood:	n/a	chr1:78440574-78440585
6	POLR2A	chr1:78440096-78441140	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:78440443-78440757	GM12892	blood:	n/a	n/a
8	EBF1	chr1:78440367-78440784	GM12878	blood:	n/a	chr1:78440574-78440585
9	POLR2A	chr1:78439465-78440747	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78439421..78442293-chr1:78443487..78445415,3	MCF-7	breast:
2	chr1:78435772..78437977-chr1:78438825..78441558,2	MCF-7	breast:

Variant related genes	Relation type
DNAJB4	TF binding region
GIPC2	TF binding region
ENSG00000162616	Chromatin interaction
ENSG00000137960	Chromatin interaction
ENSG00000162613	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1001070	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs1001103	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs1001104	0.80[AMR][1000 genomes]
rs10437022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10873956	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10873960	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162403	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162406	0.81[AMR][1000 genomes]
rs1166697	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166701	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166704	0.81[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs1166705	0.95[AMR][1000 genomes]
rs1166706	0.81[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs1166707	0.98[AMR][1000 genomes]
rs1166709	0.81[CHB][hapmap]
rs11805735	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11807240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12146104	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12723748	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1335481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536160	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539737	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1555798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616949	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1626757	0.82[AMR][1000 genomes]
rs17382996	1.00[CEU][hapmap]
rs17383213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17387365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855704	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs1971368	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2136682	0.84[EUR][1000 genomes]
rs2154138	0.81[CHB][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs2274257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4370803	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4372306	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57421725	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628451	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs638335	0.89[CHB][hapmap]
rs6424640	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424650	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424660	0.84[AMR][1000 genomes]
rs6424664	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[AMR][1000 genomes]
rs661038	0.88[CHB][hapmap]
rs6656888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6659045	0.80[AMR][1000 genomes]
rs6667733	0.80[AMR][1000 genomes]
rs6677890	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[AMR][1000 genomes]
rs7417104	0.81[CHB][hapmap]
rs750720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514007	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes]
rs7538210	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7544892	0.80[AMR][1000 genomes]
rs9324166	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9659938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9661193	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9730688	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]

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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 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	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
2	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:78418400-78440800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:78424600-78440600	Weak transcription	Stomach Mucosa	stomach
5	chr1:78429600-78441800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:78430800-78440800	Weak transcription	Psoas Muscle	Psoas
7	chr1:78432200-78441400	Weak transcription	Thymus	Thymus
8	chr1:78432200-78442400	Weak transcription	Esophagus	oesophagus
9	chr1:78432400-78440600	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:78432400-78440800	Weak transcription	Brain Germinal Matrix	brain
11	chr1:78432400-78441200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:78432400-78441200	Weak transcription	Aorta	Aorta
13	chr1:78432400-78442200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:78432400-78442400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:78432400-78442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:78432600-78443400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:78432800-78441400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:78433000-78440600	Weak transcription	Fetal Heart	heart
19	chr1:78433000-78440600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:78433200-78440600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:78433800-78440800	Weak transcription	Brain Substantia Nigra	brain
22	chr1:78433800-78441600	Weak transcription	Colonic Mucosa	Colon
23	chr1:78433800-78443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:78434800-78440600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:78434800-78440600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:78434800-78440600	Weak transcription	Fetal Brain Female	brain
27	chr1:78434800-78440800	Weak transcription	Fetal Lung	lung
28	chr1:78434800-78441400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:78434800-78442200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:78435200-78440800	Weak transcription	HSMMtube	muscle
31	chr1:78435200-78441200	Weak transcription	Fetal Kidney	kidney
32	chr1:78435200-78441400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:78435400-78440800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr1:78435400-78441200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:78435400-78441200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:78436600-78440800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:78436600-78441000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:78436600-78442400	Weak transcription	Gastric	stomach
39	chr1:78436800-78440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:78436800-78440600	Weak transcription	Liver	Liver
41	chr1:78436800-78440600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:78436800-78440800	Weak transcription	NH-A	brain
43	chr1:78436800-78441400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:78436800-78442200	Weak transcription	Pancreas	Pancrea
45	chr1:78437000-78442200	Weak transcription	Lung	lung
46	chr1:78437200-78442200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:78437200-78442200	Weak transcription	Placenta	Placenta
48	chr1:78437600-78442200	Weak transcription	Left Ventricle	heart
49	chr1:78438000-78440600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:78438000-78441400	Weak transcription	H1 Cell Line	embryonic stem cell

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