Variant report

Variant	rs62316048
Chromosome Location	chr4:69202012-69202013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:69148927..69150978-chr4:69199918..69202560,2	K562	blood:
2	chr4:69193856..69197351-chr4:69199834..69202897,3	K562	blood:
3	chr4:69152138..69154955-chr4:69200554..69203200,2	K562	blood:
4	chr4:69193689..69197466-chr4:69197800..69202580,8	K562	blood:
5	chr4:69197134..69202591-chr4:69207411..69211710,5	K562	blood:
6	chr4:69201801..69210708-chr4:69210917..69216982,18	MCF-7	breast:
7	chr4:69200762..69202347-chr4:69204552..69206284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083896	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs34147623	0.83[ASN][1000 genomes]
rs34346807	0.83[ASN][1000 genomes]
rs62316045	0.81[EUR][1000 genomes]
rs62316207	0.83[AMR][1000 genomes]
rs6816576	0.90[ASN][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	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv461546	chr4:69049643-69223057	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv594506	chr4:69049643-69223057	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62316048	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69176200-69203600	Strong transcription	Liver	Liver
2	chr4:69176200-69203600	Strong transcription	HSMM	muscle
3	chr4:69176200-69204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:69176200-69204200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:69176400-69203800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr4:69176400-69204000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:69176400-69204400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:69176400-69204600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:69176600-69203600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:69176600-69204600	Strong transcription	Fetal Thymus	thymus
11	chr4:69176800-69202200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:69176800-69203600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr4:69177200-69203600	Strong transcription	Placenta	Placenta
14	chr4:69177200-69203800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:69177200-69204200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:69177400-69204000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:69177800-69203800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:69178000-69203600	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr4:69178000-69205000	Strong transcription	Dnd41	blood
20	chr4:69182600-69213200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:69182800-69207200	Weak transcription	Small Intestine	intestine
22	chr4:69182800-69209200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:69183000-69207800	Weak transcription	Esophagus	oesophagus
24	chr4:69183600-69204200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:69183600-69204200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:69183800-69203600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:69183800-69204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:69184200-69204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:69184200-69204200	Weak transcription	Gastric	stomach
30	chr4:69184200-69207800	Weak transcription	Spleen	Spleen
31	chr4:69184200-69212200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:69184200-69212800	Weak transcription	Aorta	Aorta
33	chr4:69184800-69204200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:69185200-69203800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr4:69185400-69203800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:69185400-69204800	Weak transcription	Stomach Mucosa	stomach
37	chr4:69186600-69202600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr4:69186800-69203400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:69186800-69203600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr4:69186800-69203800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr4:69186800-69204200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:69187000-69203400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:69187000-69203600	Strong transcription	Fetal Intestine Large	intestine
44	chr4:69187000-69203800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:69187000-69204000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr4:69188600-69202200	Weak transcription	Thymus	Thymus
47	chr4:69188600-69204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:69188800-69204400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:69189200-69214400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:69191000-69203600	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links