Variant report

Variant	rs56296494
Chromosome Location	chr10:5918344-5918345
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5853596..5857884-chr10:5911550..5919142,12	MCF-7	breast:
2	chr10:5853453..5857248-chr10:5914833..5919853,7	K562	blood:
3	chr10:5853075..5856620-chr10:5914833..5920117,6	K562	blood:
4	chr10:5915609..5918597-chr10:5924591..5926431,2	K562	blood:
5	chr10:5912116..5916503-chr10:5917203..5921455,4	K562	blood:
6	chr10:5917302..5921893-chr10:5926757..5932751,9	MCF-7	breast:
7	chr10:5853771..5858349-chr10:5915568..5920799,8	MCF-7	breast:
8	chr10:5916960..5919162-chr10:5939258..5940829,2	K562	blood:
9	chr10:5729799..5732173-chr10:5916064..5918790,2	MCF-7	breast:
10	chr10:5913737..5922370-chr10:5922961..5932189,19	K562	blood:
11	chr10:5912111..5919800-chr10:5923492..5927477,10	MCF-7	breast:
12	chr10:5912116..5915465-chr10:5917203..5919997,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134452	Chromatin interaction
ENSG00000057608	Chromatin interaction
ENSG00000272764	Chromatin interaction
ENSG00000134461	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11592964	1.00[AFR][1000 genomes]
rs11594153	1.00[AFR][1000 genomes]
rs11594794	0.86[ASN][1000 genomes]
rs11595457	1.00[AFR][1000 genomes]
rs11598581	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11598865	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11813102	0.87[EUR][1000 genomes]
rs17146333	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17146580	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17146587	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17146629	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031230	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2137422	1.00[AFR][1000 genomes]
rs2274026	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274027	0.86[ASN][1000 genomes]
rs2274028	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2274031	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2274033	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296136	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296137	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2296138	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34249852	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34455477	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750659	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41290311	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41306916	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4749325	1.00[AFR][1000 genomes]
rs4749407	1.00[AFR][1000 genomes]
rs55718140	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56103646	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56333805	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56354230	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61834499	0.86[ASN][1000 genomes]
rs7893821	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7899635	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7899847	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7902223	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7904512	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7904712	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7912210	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7913876	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7918162	0.87[ASN][1000 genomes]
rs7919410	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7923781	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5903400-5925000	Weak transcription	Fetal Kidney	kidney
2	chr10:5908800-5918400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr10:5909600-5924800	Weak transcription	Stomach Mucosa	stomach
4	chr10:5911600-5919800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:5911600-5926800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr10:5913000-5929800	Weak transcription	Fetal Heart	heart
7	chr10:5913000-5929800	Weak transcription	Psoas Muscle	Psoas
8	chr10:5914000-5929600	Weak transcription	NHLF	lung
9	chr10:5914600-5918400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr10:5915600-5924400	Weak transcription	Fetal Brain Male	brain
11	chr10:5915600-5930000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:5915600-5930000	Weak transcription	HUVEC	blood vessel
13	chr10:5915800-5919600	Weak transcription	Hela-S3	cervix
14	chr10:5915800-5920000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:5915800-5930000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:5915800-5930200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr10:5916000-5921000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr10:5916200-5918400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:5916200-5919200	Strong transcription	Aorta	Aorta
20	chr10:5916200-5920400	Strong transcription	Rectal Smooth Muscle	rectum
21	chr10:5916200-5920600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr10:5916200-5921200	Strong transcription	Colon Smooth Muscle	Colon
23	chr10:5916200-5922000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:5916200-5922200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:5916200-5922800	Strong transcription	Fetal Stomach	stomach
26	chr10:5916200-5923000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:5916200-5923000	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr10:5916200-5923000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr10:5916200-5925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:5916200-5926400	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:5916200-5927600	Strong transcription	Fetal Intestine Small	intestine
32	chr10:5916200-5928200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:5916200-5929000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr10:5916200-5929400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr10:5916200-5929800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr10:5916200-5929800	Strong transcription	Fetal Intestine Large	intestine
37	chr10:5916400-5918400	Weak transcription	K562	blood
38	chr10:5916400-5920400	Strong transcription	Ovary	ovary
39	chr10:5916400-5922000	Strong transcription	Fetal Muscle Leg	muscle
40	chr10:5916400-5922200	Strong transcription	Left Ventricle	heart
41	chr10:5916400-5922400	Weak transcription	Primary B cells from cord blood	blood
42	chr10:5916400-5923000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr10:5916400-5924800	Strong transcription	Liver	Liver
44	chr10:5916400-5928200	Strong transcription	Fetal Brain Female	brain
45	chr10:5916400-5929200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr10:5916400-5929800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr10:5916600-5922000	Strong transcription	Gastric	stomach
48	chr10:5916600-5922400	Strong transcription	Brain Substantia Nigra	brain
49	chr10:5916600-5928400	Weak transcription	Small Intestine	intestine
50	chr10:5916600-5929400	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links