Variant report

Variant	rs57421725
Chromosome Location	chr1:78437645-78437646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78435772..78437977-chr1:78438825..78441558,2	MCF-7	breast:
2	chr1:78224281..78226178-chr1:78436079..78437908,2	K562	blood:
3	chr1:78436988..78440391-chr1:78442144..78445660,4	MCF-7	breast:
4	chr1:78432055..78439376-chr1:78440995..78447364,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137960	Chromatin interaction
ENSG00000077254	Chromatin interaction
ENSG00000162616	Chromatin interaction
ENSG00000162613	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1001104	0.80[AMR][1000 genomes]
rs10437022	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10873956	0.80[AMR][1000 genomes]
rs10873960	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162400	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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166702	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1166704	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1166705	0.95[AMR][1000 genomes]
rs1166706	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1166707	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11805735	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11807240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12146104	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405212	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12409561	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723748	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1335481	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1536160	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555798	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616949	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1626757	0.82[AMR][1000 genomes]
rs17383213	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17387365	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971368	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2136682	0.84[EUR][1000 genomes]
rs2154138	0.80[AMR][1000 genomes]
rs2274257	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296453	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767028	0.96[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	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949828	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949829	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6424640	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6424650	0.89[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	0.80[AMR][1000 genomes]
rs6656888	0.89[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	0.80[AMR][1000 genomes]
rs750720	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514007	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	0.96[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	chr1:78407400-78437800	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:78411800-78438200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:78415800-78440200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:78416400-78438200	Strong transcription	HMEC	breast
8	chr1:78417200-78438000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:78418400-78438000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:78418400-78438200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:78418400-78440800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:78420800-78438200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:78421200-78437800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:78424600-78440600	Weak transcription	Stomach Mucosa	stomach
15	chr1:78426400-78439600	Weak transcription	Spleen	Spleen
16	chr1:78428600-78438200	Strong transcription	Fetal Intestine Large	intestine
17	chr1:78429600-78441800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:78430200-78438600	Strong transcription	NHEK	skin
19	chr1:78430800-78440800	Weak transcription	Psoas Muscle	Psoas
20	chr1:78432200-78441400	Weak transcription	Thymus	Thymus
21	chr1:78432200-78442400	Weak transcription	Esophagus	oesophagus
22	chr1:78432400-78439000	Weak transcription	Fetal Stomach	stomach
23	chr1:78432400-78440600	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:78432400-78440800	Weak transcription	Brain Germinal Matrix	brain
25	chr1:78432400-78441200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:78432400-78441200	Weak transcription	Aorta	Aorta
27	chr1:78432400-78442200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:78432400-78442400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:78432400-78442400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:78432600-78438000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:78432600-78440000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:78432600-78443400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:78432800-78441400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:78433000-78440600	Weak transcription	Fetal Heart	heart
35	chr1:78433000-78440600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:78433200-78440600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:78433600-78438200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr1:78433800-78440800	Weak transcription	Brain Substantia Nigra	brain
39	chr1:78433800-78441600	Weak transcription	Colonic Mucosa	Colon
40	chr1:78433800-78443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:78434800-78439400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:78434800-78440000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:78434800-78440200	Weak transcription	NHLF	lung
44	chr1:78434800-78440600	Weak transcription	Brain Angular Gyrus	brain
45	chr1:78434800-78440600	Weak transcription	Brain Anterior Caudate	brain
46	chr1:78434800-78440600	Weak transcription	Fetal Brain Female	brain
47	chr1:78434800-78440800	Weak transcription	Fetal Lung	lung
48	chr1:78434800-78441400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:78434800-78442200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:78435000-78437800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links