Variant report

Variant	rs5030558
Chromosome Location	chr4:110618066-110618067
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110617659..110620407-chr4:110623274..110624827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11930714	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11932341	1.00[AMR][1000 genomes]
rs11933017	1.00[AMR][1000 genomes]
rs11936584	1.00[AMR][1000 genomes]
rs11941981	1.00[EUR][1000 genomes]
rs11945658	1.00[AMR][1000 genomes]
rs11947977	1.00[AMR][1000 genomes]
rs17040661	1.00[AMR][1000 genomes]
rs17040705	1.00[AMR][1000 genomes]
rs17040707	1.00[AMR][1000 genomes]
rs17040741	1.00[AMR][1000 genomes]
rs17040795	1.00[EUR][1000 genomes]
rs4582151	1.00[AMR][1000 genomes]
rs5030568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5030569	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5030574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5030583	1.00[EUR][1000 genomes]
rs5030586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers 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 miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv595142	chr4:110609481-110656730	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr4:110572600-110623200	Weak transcription	Esophagus	oesophagus
2	chr4:110589600-110623200	Weak transcription	Brain Substantia Nigra	brain
3	chr4:110598800-110622800	Weak transcription	NHEK	skin
4	chr4:110600800-110622600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:110601800-110622800	Weak transcription	Right Atrium	heart
6	chr4:110602600-110620000	Weak transcription	Small Intestine	intestine
7	chr4:110605000-110622800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:110605200-110619800	Strong transcription	Dnd41	blood
9	chr4:110605600-110619800	Strong transcription	Fetal Thymus	thymus
10	chr4:110605600-110622800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:110605800-110619400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:110605800-110622800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:110606400-110622800	Weak transcription	Hela-S3	cervix
14	chr4:110607200-110622800	Weak transcription	Fetal Brain Male	brain
15	chr4:110607400-110618600	Strong transcription	Fetal Intestine Small	intestine
16	chr4:110607600-110619000	Strong transcription	Fetal Intestine Large	intestine
17	chr4:110607800-110623200	Weak transcription	Brain Angular Gyrus	brain
18	chr4:110608400-110618800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr4:110608600-110619400	Strong transcription	Liver	Liver
20	chr4:110608800-110619200	Strong transcription	Adipose Nuclei	Adipose
21	chr4:110609000-110622800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:110609600-110623000	Weak transcription	A549	lung
23	chr4:110609800-110619600	Weak transcription	HepG2	liver
24	chr4:110609800-110623200	Weak transcription	Psoas Muscle	Psoas
25	chr4:110610000-110619400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:110610200-110619400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:110610200-110619400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr4:110610200-110619400	Strong transcription	Fetal Muscle Leg	muscle
29	chr4:110610400-110618800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr4:110611000-110619600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr4:110611000-110623200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:110611200-110621600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:110611200-110623800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:110611400-110619400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr4:110611400-110619400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:110611400-110619800	Strong transcription	Fetal Lung	lung
37	chr4:110611600-110622600	Weak transcription	Fetal Heart	heart
38	chr4:110611600-110623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:110611800-110619600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:110612200-110622800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:110612200-110623000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:110612400-110622800	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:110613000-110619200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:110613000-110623200	Weak transcription	Brain Anterior Caudate	brain
45	chr4:110613200-110619000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:110613200-110619200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr4:110613200-110619800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:110613200-110622400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr4:110613600-110619400	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr4:110613600-110620000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links