Variant report

Variant	rs628175
Chromosome Location	chr10:5916104-5916105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5900574..5904581-chr10:5915498..5917338,4	MCF-7	breast:
2	chr10:5725838..5728251-chr10:5915424..5916991,2	MCF-7	breast:
3	chr10:5853596..5857884-chr10:5911550..5919142,12	MCF-7	breast:
4	chr10:5910241..5913072-chr10:5913979..5917301,3	MCF-7	breast:
5	chr10:5912116..5916503-chr10:5917203..5921455,4	K562	blood:
6	chr10:5914288..5916815-chr10:5925333..5927218,2	MCF-7	breast:
7	chr10:5853453..5857248-chr10:5914833..5919853,7	K562	blood:
8	chr10:5853075..5856620-chr10:5914833..5920117,6	K562	blood:
9	chr10:5915609..5918597-chr10:5924591..5926431,2	K562	blood:
10	chr10:5853771..5858349-chr10:5915568..5920799,8	MCF-7	breast:
11	chr10:5913606..5917218-chr10:5929180..5932208,4	MCF-7	breast:
12	chr10:5729799..5732173-chr10:5916064..5918790,2	MCF-7	breast:
13	chr10:5913737..5922370-chr10:5922961..5932189,19	K562	blood:
14	chr10:5912111..5919800-chr10:5923492..5927477,10	MCF-7	breast:
15	chr10:5900731..5902492-chr10:5915568..5917160,2	K562	blood:
16	chr10:5816149..5818545-chr10:5914813..5916683,2	MCF-7	breast:
17	chr10:5850191..5852972-chr10:5915096..5916950,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000240180	Chromatin interaction
ENSG00000134452	Chromatin interaction
ENSG00000134461	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000108021	Chromatin interaction
ENSG00000270427	Chromatin interaction
ENSG00000272764	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1052420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1323659	0.83[EUR][1000 genomes]
rs1707228	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2669124	0.95[ASN][1000 genomes]
rs2761269	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2942348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2985043	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2985044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs584000	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs587620	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587655	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs593026	0.95[ASN][1000 genomes]
rs596156	0.95[ASN][1000 genomes]
rs599394	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600706	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs608197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609269	0.95[ASN][1000 genomes]
rs610335	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615879	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617165	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622252	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622488	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625073	0.94[ASN][1000 genomes]
rs626040	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627303	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs628219	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628234	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628844	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631538	0.87[ASN][1000 genomes]
rs631947	0.83[EUR][1000 genomes]
rs644474	0.90[ASN][1000 genomes]
rs646406	0.95[ASN][1000 genomes]
rs646490	0.97[ASN][1000 genomes]
rs647391	0.97[ASN][1000 genomes]
rs661411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs662701	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs664577	0.95[ASN][1000 genomes]
rs664842	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs666831	0.95[ASN][1000 genomes]
rs672219	0.87[ASN][1000 genomes]
rs672624	0.84[ASN][1000 genomes]
rs673496	0.95[ASN][1000 genomes]
rs673678	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675416	0.95[ASN][1000 genomes]
rs679610	0.97[ASN][1000 genomes]
rs682555	0.84[EUR][1000 genomes]
rs684557	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs687191	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs792342	0.95[ASN][1000 genomes]
rs792347	0.95[ASN][1000 genomes]
rs792349	0.95[ASN][1000 genomes]
rs811561	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9329328	0.95[ASN][1000 genomes]
rs9424023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv5654	chr10:5868365-5930634	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv825229	chr10:5886905-5967697	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv466722	chr10:5893268-5916201	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv549904	chr10:5893268-5916201	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5894600-5916800	Weak transcription	Spleen	Spleen
2	chr10:5896400-5918200	Weak transcription	Fetal Lung	lung
3	chr10:5900000-5916600	Weak transcription	Pancreas	Pancrea
4	chr10:5900400-5916200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:5900600-5916200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr10:5901000-5916600	Weak transcription	Gastric	stomach
7	chr10:5901200-5918200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:5902400-5918200	Weak transcription	Primary T cells from cord blood	blood
9	chr10:5902800-5916200	Weak transcription	Fetal Intestine Large	intestine
10	chr10:5902800-5916600	Weak transcription	Brain Substantia Nigra	brain
11	chr10:5902800-5918000	Weak transcription	Lung	lung
12	chr10:5903400-5918200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr10:5903400-5925000	Weak transcription	Fetal Kidney	kidney
14	chr10:5903600-5916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:5903800-5916400	Weak transcription	A549	lung
16	chr10:5903800-5918200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:5904400-5916200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:5904400-5916200	Weak transcription	Aorta	Aorta
19	chr10:5904600-5916200	Weak transcription	NHDF-Ad	bronchial
20	chr10:5905000-5916200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr10:5905000-5916200	Weak transcription	Brain Angular Gyrus	brain
22	chr10:5905200-5918200	Weak transcription	HepG2	liver
23	chr10:5908800-5918400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr10:5909400-5916400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr10:5909400-5918200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr10:5909600-5924800	Weak transcription	Stomach Mucosa	stomach
27	chr10:5909800-5918200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr10:5910600-5916600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr10:5911000-5916200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:5911200-5916200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:5911200-5918200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:5911400-5916200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr10:5911400-5916200	Weak transcription	Colon Smooth Muscle	Colon
34	chr10:5911400-5918200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr10:5911600-5916200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr10:5911600-5916200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr10:5911600-5916400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:5911600-5916400	Weak transcription	Fetal Brain Female	brain
39	chr10:5911600-5916600	Weak transcription	Brain Germinal Matrix	brain
40	chr10:5911600-5918200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:5911600-5919800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr10:5911600-5926800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr10:5912000-5916200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr10:5912200-5916200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:5912600-5918200	Weak transcription	HMEC	breast
46	chr10:5912800-5916200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr10:5912800-5916400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr10:5912800-5916400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr10:5913000-5916200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr10:5913000-5916200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links