Variant report

Variant	rs13123803
Chromosome Location	chr4:57176710-57176711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57175601..57178505-chr4:57178570..57181893,3	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11721942	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049087	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2049089	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58975286	0.81[AMR][1000 genomes]
rs9996593	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS 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	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13123803	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57149400-57179400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:57156800-57177800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:57162800-57189400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:57163000-57177800	Weak transcription	Colonic Mucosa	Colon
5	chr4:57163000-57184000	Weak transcription	Right Atrium	heart
6	chr4:57163400-57180400	Weak transcription	Pancreas	Pancrea
7	chr4:57167600-57179600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:57167600-57203400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:57167800-57177000	Weak transcription	Brain Substantia Nigra	brain
10	chr4:57167800-57178800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:57167800-57179000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
13	chr4:57168000-57177000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:57168400-57179600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:57168600-57179200	Weak transcription	Ovary	ovary
16	chr4:57171000-57187400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:57172000-57180000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:57172000-57204000	Weak transcription	Stomach Mucosa	stomach
19	chr4:57172600-57179800	Weak transcription	Placenta	Placenta
20	chr4:57172600-57180000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:57173000-57180200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:57173200-57202800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:57173600-57180000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:57173800-57177600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:57173800-57182600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr4:57173800-57185200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:57174400-57179400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:57174400-57195000	Strong transcription	Fetal Intestine Small	intestine
29	chr4:57174400-57203800	Weak transcription	Fetal Kidney	kidney
30	chr4:57174600-57179000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:57174600-57180200	Strong transcription	Fetal Intestine Large	intestine
32	chr4:57174600-57182200	Weak transcription	HepG2	liver
33	chr4:57174600-57197200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:57175000-57177000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:57175000-57179400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:57175200-57177400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:57175800-57177400	Weak transcription	Fetal Stomach	stomach
38	chr4:57175800-57179600	Enhancers	Brain Germinal Matrix	brain
39	chr4:57176000-57177800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:57176000-57178600	Enhancers	Fetal Brain Male	brain
41	chr4:57176000-57183400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr4:57176000-57190000	Weak transcription	Gastric	stomach
43	chr4:57176200-57176800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:57176200-57176800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:57176200-57178200	Enhancers	Brain Anterior Caudate	brain
46	chr4:57176400-57176800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:57176400-57176800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:57176400-57177400	Weak transcription	Brain Angular Gyrus	brain
49	chr4:57176400-57177600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:57176400-57178200	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links