Variant report

Variant	rs4253038
Chromosome Location	chr10:50736979-50736980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50727908..50731629-chr10:50735183..50738136,3	MCF-7	breast:
2	chr10:50729482..50733326-chr10:50734602..50739448,5	K562	blood:
3	chr10:50731383..50733326-chr10:50736507..50739448,3	K562	blood:

Variant related genes	Relation type
ENSG00000243251	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10776575	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857497	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857504	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857506	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11101144	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101155	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2177819	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2229760	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2281792	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2377900	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3750747	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793784	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4253160	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4253190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4253234	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7895633	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9971208	0.87[ASN][1000 genomes]
rs9988727	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4253038	ERCC6	cis	cerebellum	SCAN
rs4253038	ERCC6	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50717200-50746000	Weak transcription	Fetal Heart	heart
2	chr10:50717400-50737000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr10:50720400-50746200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:50723000-50741000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr10:50723200-50741000	Strong transcription	Primary T cells from cord blood	blood
6	chr10:50723200-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:50723200-50741000	Strong transcription	HMEC	breast
8	chr10:50723200-50741800	Strong transcription	Osteobl	bone
9	chr10:50723400-50739600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr10:50723400-50741000	Strong transcription	Fetal Intestine Large	intestine
11	chr10:50723400-50741000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr10:50723400-50741600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr10:50723400-50741600	Strong transcription	NHEK	skin
14	chr10:50723600-50741000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr10:50725000-50746200	Weak transcription	Psoas Muscle	Psoas
16	chr10:50726800-50739600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:50727800-50741000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:50727800-50741000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:50727800-50741000	Strong transcription	Adipose Nuclei	Adipose
20	chr10:50727800-50741200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:50728200-50741000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr10:50728200-50741400	Strong transcription	HSMM	muscle
23	chr10:50728400-50738600	Strong transcription	Fetal Thymus	thymus
24	chr10:50728400-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:50728400-50741000	Strong transcription	Placenta	Placenta
26	chr10:50728600-50740600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr10:50728600-50741400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:50728800-50741000	Strong transcription	Dnd41	blood
29	chr10:50728800-50742000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr10:50729000-50745800	Weak transcription	Stomach Mucosa	stomach
31	chr10:50729200-50738600	Strong transcription	Fetal Muscle Leg	muscle
32	chr10:50729200-50741400	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr10:50729200-50742400	Strong transcription	Hela-S3	cervix
34	chr10:50729600-50740000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:50730000-50737400	Weak transcription	Right Atrium	heart
36	chr10:50730000-50746400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr10:50730600-50741000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr10:50730600-50741200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:50730800-50741000	Strong transcription	Ovary	ovary
40	chr10:50730800-50741400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr10:50731000-50738600	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr10:50731000-50740400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr10:50731000-50741400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr10:50731200-50738200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr10:50731200-50738400	Strong transcription	HSMMtube	muscle
46	chr10:50731200-50738600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr10:50731200-50740800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr10:50731200-50741000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:50731400-50738600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr10:50731400-50740600	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links