Variant report

Variant	rs6812178
Chromosome Location	chr4:69200559-69200560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:69197759-69200824	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

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	chr4:69188337..69192029-chr4:69196790..69201126,5	K562	blood:
7	chr4:69188337..69191371-chr4:69197664..69201126,3	K562	blood:
8	chr4:69198525..69201741-chr4:69214213..69215986,3	MCF-7	breast:

No data

Variant related genes	Relation type
YTHDC1	TF binding region
ENSG00000083896	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10033058	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726194	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727878	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124352	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130430	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1406694	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17089252	0.81[ASN][1000 genomes]
rs17089267	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1715080	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1715081	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1730873	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1919898	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293594	0.82[ASN][1000 genomes]
rs2293595	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2319888	0.84[ASN][1000 genomes]
rs2319891	0.80[ASN][1000 genomes]
rs28656921	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34419508	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34452677	0.82[ASN][1000 genomes]
rs34500620	0.82[ASN][1000 genomes]
rs35632454	0.82[ASN][1000 genomes]
rs36098059	0.82[ASN][1000 genomes]
rs3797008	0.82[ASN][1000 genomes]
rs4428356	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4860929	0.81[ASN][1000 genomes]
rs56283078	0.84[ASN][1000 genomes]
rs57105149	0.83[ASN][1000 genomes]
rs57643586	0.85[ASN][1000 genomes]
rs58108365	0.85[ASN][1000 genomes]
rs62316045	0.85[ASN][1000 genomes]
rs7666993	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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
rs6812178	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	chr4:69177800-69201200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:69177800-69203800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr4:69178000-69203600	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr4:69178000-69205000	Strong transcription	Dnd41	blood
21	chr4:69182600-69213200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:69182800-69207200	Weak transcription	Small Intestine	intestine
23	chr4:69182800-69209200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:69183000-69207800	Weak transcription	Esophagus	oesophagus
25	chr4:69183400-69200600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr4:69183600-69204200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:69183600-69204200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:69183800-69203600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:69183800-69204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:69184200-69204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:69184200-69204200	Weak transcription	Gastric	stomach
32	chr4:69184200-69207800	Weak transcription	Spleen	Spleen
33	chr4:69184200-69212200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:69184200-69212800	Weak transcription	Aorta	Aorta
35	chr4:69184800-69204200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:69185200-69203800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:69185400-69203800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:69185400-69204800	Weak transcription	Stomach Mucosa	stomach
39	chr4:69186600-69200600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr4:69186600-69202600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:69186800-69203400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:69186800-69203600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:69186800-69203800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr4:69186800-69204200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:69187000-69203400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:69187000-69203600	Strong transcription	Fetal Intestine Large	intestine
47	chr4:69187000-69203800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:69187000-69204000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr4:69188600-69202200	Weak transcription	Thymus	Thymus
50	chr4:69188600-69204200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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