Variant report

Variant	rs4475708
Chromosome Location	chr1:179555947-179555948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:179555176-179555982	MCF-7	breast:	n/a	n/a
2	HA-E2F1	chr1:179555139-179556249	MCF-7	breast:	n/a	chr1:179555739-179555746 chr1:179555147-179555156
3	EGR1	chr1:179555360-179555966	H1-hESC	embryonic stem cell:	n/a	chr1:179555414-179555427
4	TBP	chr1:179555330-179556014	H1-hESC	embryonic stem cell:	n/a	n/a
5	HDAC2	chr1:179555255-179556159	MCF-7	breast:	n/a	n/a
6	EGR1	chr1:179555510-179556024	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr1:179555013-179556347	SK-N-SH	brain:	n/a	chr1:179555549-179555562
8	NFIC	chr1:179555373-179556081	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr1:179555325-179556051	ECC-1	luminal epithelium:	n/a	n/a
10	EGR1	chr1:179555552-179555960	K562	blood:	n/a	n/a
11	CTCF	chr1:179555243-179555963	MCF-7	breast:	n/a	chr1:179555549-179555562
12	MAX	chr1:179555371-179556176	MCF-7	breast:	n/a	n/a
13	FOXA2	chr1:179555342-179555981	A549	lung:	n/a	n/a
14	EGR1	chr1:179555507-179555999	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr1:179554976-179556053	A549	lung:	n/a	chr1:179555549-179555562
16	TCF12	chr1:179555321-179555976	ECC-1	luminal epithelium:	n/a	n/a
17	EGR1	chr1:179555459-179556086	MCF-7	breast:	n/a	n/a
18	ZNF263	chr1:179555408-179556120	HEK293-T-REx	kidney:	n/a	n/a
19	MXI1	chr1:179554800-179556213	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179543048..179545135-chr1:179554204..179557043,2	K562	blood:
2	chr1:179553040..179558877-chr1:179559940..179564416,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPHS2-2	chr1:179555798-179556543	NONHSAT007869

Variant related genes	Relation type
TDRD5	TF binding region
ENSG00000261060	TF binding region
ENSG00000116218	Chromatin interaction
ENSG00000162782	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10753199	0.98[EUR][1000 genomes]
rs6691184	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4475708	TDRD5	cis	Thyroid	GTEx
rs4475708	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs4475708	TDRD5	cis	Nerve Tibial	GTEx
rs4475708	TDRD5	cis	Artery Aorta	GTEx
rs4475708	TDRD5	cis	Adipose Subcutaneous	GTEx
rs4475708	TDRD5	cis	Esophagus Mucosa	GTEx
rs4475708	RP11-545A16.4	cis	Artery Tibial	GTEx
rs4475708	TDRD5	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179555000-179556000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:179555000-179556000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:179555000-179556000	Active TSS	Brain Cingulate Gyrus	brain
4	chr1:179555000-179556000	Active TSS	Fetal Brain Female	brain
5	chr1:179555000-179556000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:179555000-179556200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:179555000-179556200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:179555000-179556200	Enhancers	Fetal Brain Male	brain
9	chr1:179555000-179556200	Active TSS	Rectal Smooth Muscle	rectum
10	chr1:179555200-179556000	Active TSS	H9 Cell Line	embryonic stem cell
11	chr1:179555200-179556000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:179555200-179556000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:179555200-179556000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:179555200-179556000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:179555200-179556000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:179555200-179556000	Active TSS	Brain Angular Gyrus	brain
17	chr1:179555200-179556000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:179555200-179556000	Active TSS	Duodenum Mucosa	Duodenum
19	chr1:179555200-179556000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:179555200-179556000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
21	chr1:179555200-179556000	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr1:179555200-179556000	Active TSS	Right Atrium	heart
23	chr1:179555200-179556000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
24	chr1:179555200-179556000	Active TSS	HSMM	muscle
25	chr1:179555200-179556000	Bivalent/Poised TSS	K562	blood
26	chr1:179555200-179556000	Bivalent/Poised TSS	NHEK	skin
27	chr1:179555200-179556200	Active TSS	Brain Anterior Caudate	brain
28	chr1:179555200-179556200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr1:179555200-179556200	Active TSS	A549	lung
30	chr1:179555400-179556000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr1:179555400-179556000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:179555400-179556000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr1:179555400-179556000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:179555400-179556000	Active TSS	Adipose Nuclei	Adipose
35	chr1:179555400-179556000	Enhancers	Liver	Liver
36	chr1:179555400-179556000	Active TSS	Brain Substantia Nigra	brain
37	chr1:179555400-179556000	Flanking Active TSS	Colonic Mucosa	Colon
38	chr1:179555400-179556000	Active TSS	Colon Smooth Muscle	Colon
39	chr1:179555400-179556000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr1:179555400-179556000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
41	chr1:179555400-179556000	Active TSS	Fetal Intestine Small	intestine
42	chr1:179555400-179556000	Flanking Active TSS	Ovary	ovary
43	chr1:179555400-179556000	Active TSS	Pancreas	Pancrea
44	chr1:179555400-179556000	Active TSS	HSMMtube	muscle
45	chr1:179555600-179556000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:179555600-179556000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:179555600-179556000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:179555600-179556000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr1:179555600-179556000	Bivalent Enhancer	Thymus	Thymus
50	chr1:179555600-179556200	Active TSS	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links