Variant report

Variant	rs10520279
Chromosome Location	chr4:175234429-175234430
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:175203956..175205751-chr4:175232556..175234704,2	K562	blood:

Variant related genes	Relation type
ENSG00000164118	Chromatin interaction
ENSG00000164117	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10434410	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10520278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13122347	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134635	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13137178	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs1396193	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17060404	0.80[ASN][1000 genomes]
rs17060428	0.82[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17060454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35190385	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35593724	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36081616	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62335793	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335798	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6553781	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs66919862	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72621998	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7671444	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7684619	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696841	0.80[ASN][1000 genomes]
rs906569	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs906570	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs9715080	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv869116	chr4:175231090-175801761	Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175205600-175241600	Weak transcription	Small Intestine	intestine
2	chr4:175206000-175235000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:175206200-175241000	Weak transcription	Right Ventricle	heart
4	chr4:175206600-175237800	Weak transcription	Osteobl	bone
5	chr4:175206800-175241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:175207000-175239000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:175207000-175240000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:175207000-175242000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:175214200-175239200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:175214600-175236000	Weak transcription	A549	lung
11	chr4:175214600-175237200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:175214600-175237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:175214600-175238000	Weak transcription	HMEC	breast
14	chr4:175214600-175238400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:175214600-175238800	Weak transcription	Aorta	Aorta
16	chr4:175214600-175239000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:175214600-175239000	Weak transcription	HepG2	liver
18	chr4:175214600-175240000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:175214600-175240200	Weak transcription	Brain Angular Gyrus	brain
20	chr4:175214600-175240600	Weak transcription	Fetal Stomach	stomach
21	chr4:175214600-175241600	Weak transcription	Lung	lung
22	chr4:175214600-175241600	Weak transcription	Thymus	Thymus
23	chr4:175214600-175241800	Weak transcription	Pancreas	Pancrea
24	chr4:175214600-175242000	Weak transcription	Brain Substantia Nigra	brain
25	chr4:175214600-175243200	Weak transcription	Ovary	ovary
26	chr4:175214600-175244800	Weak transcription	Psoas Muscle	Psoas
27	chr4:175214600-175245400	Weak transcription	HSMM	muscle
28	chr4:175214600-175254800	Weak transcription	Esophagus	oesophagus
29	chr4:175214800-175239200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:175214800-175240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:175214800-175241200	Weak transcription	Brain Anterior Caudate	brain
32	chr4:175215000-175235800	Weak transcription	Hela-S3	cervix
33	chr4:175215200-175241600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:175215200-175242600	Weak transcription	GM12878-XiMat	blood
35	chr4:175217600-175241600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:175217800-175240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:175218600-175242000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:175219000-175239600	Weak transcription	Fetal Brain Female	brain
39	chr4:175219000-175242800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:175219400-175235800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:175219600-175235600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:175219600-175237800	Weak transcription	HUVEC	blood vessel
43	chr4:175220000-175234600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:175221400-175239200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:175221600-175240600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:175222400-175242000	Weak transcription	Fetal Intestine Small	intestine
47	chr4:175222600-175241400	Weak transcription	Spleen	Spleen
48	chr4:175224400-175234600	Strong transcription	Fetal Thymus	thymus
49	chr4:175225000-175237600	Weak transcription	NH-A	brain
50	chr4:175225400-175241800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links