Variant report

Variant	rs28475404
Chromosome Location	chr10:52177612-52177613
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52176233..52179172-chr10:52229395..52232901,6	MCF-7	breast:
2	chr10:52176817..52177809-chr11:65271375..65272246,2	Hela-S3	cervix:
3	chr10:52176588..52178104-chr10:52321160..52323318,2	MCF-7	breast:
4	chr10:52173595..52180106-chr10:52381535..52385847,7	MCF-7	breast:
5	chr10:52177364..52178170-chr6:2999684..3000477,2	Hela-S3	cervix:
6	chr10:52173619..52179913-chr10:52381938..52386991,6	K562	blood:
7	chr10:52152378..52155454-chr10:52174313..52178963,4	MCF-7	breast:
8	chr10:52177553..52178230-chr9:34179387..34179965,2	Hela-S3	cervix:
9	chr10:52173349..52175159-chr10:52175578..52178225,2	K562	blood:
10	chr10:52152624..52157680-chr10:52173844..52179255,6	K562	blood:
11	chr10:52176732..52178529-chr10:52382760..52384432,2	MCF-7	breast:
12	chr10:52136978..52138506-chr10:52174976..52177884,2	K562	blood:
13	chr10:52174976..52177960-chr10:52379518..52382234,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269700	Chromatin interaction
ENSG00000225303	Chromatin interaction
ENSG00000198964	Chromatin interaction
ENSG00000226200	Chromatin interaction
ENSG00000124588	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4935595	1.00[AMR][1000 genomes]
rs74131296	1.00[AFR][1000 genomes]
rs9943298	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv948006	chr10:52127164-52177684	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 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	chr10:52170400-52178400	Active TSS	GM12878-XiMat	blood
2	chr10:52175200-52177800	Flanking Active TSS	Liver	Liver
3	chr10:52175600-52178400	Active TSS	Fetal Kidney	kidney
4	chr10:52176000-52178400	Active TSS	Brain Cingulate Gyrus	brain
5	chr10:52176000-52178400	Active TSS	Placenta	Placenta
6	chr10:52176200-52178400	Active TSS	Hela-S3	cervix
7	chr10:52176200-52178800	Active TSS	Right Atrium	heart
8	chr10:52176200-52178800	Active TSS	NHDF-Ad	bronchial
9	chr10:52176400-52178400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:52176400-52178800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:52176400-52178800	Active TSS	HSMMtube	muscle
12	chr10:52176600-52178400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr10:52176600-52178400	Active TSS	HSMM	muscle
14	chr10:52176600-52178600	Active TSS	Fetal Muscle Trunk	muscle
15	chr10:52176600-52178800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:52176600-52178800	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr10:52176600-52178800	Active TSS	Colon Smooth Muscle	Colon
18	chr10:52176600-52178800	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr10:52176800-52177800	Active TSS	Thymus	Thymus
20	chr10:52176800-52178200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:52176800-52178400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr10:52176800-52178400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:52176800-52178400	Active TSS	Brain Angular Gyrus	brain
24	chr10:52176800-52178400	Active TSS	Ovary	ovary
25	chr10:52176800-52178600	Active TSS	Aorta	Aorta
26	chr10:52176800-52178600	Active TSS	Left Ventricle	heart
27	chr10:52176800-52178600	Active TSS	Lung	lung
28	chr10:52176800-52178600	Active TSS	Right Ventricle	heart
29	chr10:52176800-52178800	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr10:52176800-52179000	Active TSS	Stomach Smooth Muscle	stomach
31	chr10:52177000-52178400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr10:52177000-52178400	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr10:52177000-52178400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr10:52177000-52178400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr10:52177000-52178400	Active TSS	Brain Anterior Caudate	brain
36	chr10:52177000-52178400	Active TSS	Brain Hippocampus Middle	brain
37	chr10:52177000-52178400	Active TSS	HMEC	breast
38	chr10:52177000-52178400	Active TSS	NHEK	skin
39	chr10:52177000-52178600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:52177000-52178600	Active TSS	Brain Substantia Nigra	brain
41	chr10:52177000-52178800	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr10:52177000-52178800	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr10:52177000-52179000	Active TSS	A549	lung
44	chr10:52177200-52177800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr10:52177200-52177800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr10:52177200-52177800	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr10:52177200-52177800	Flanking Active TSS	HepG2	liver
48	chr10:52177200-52178200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr10:52177200-52178400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr10:52177200-52178400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links