Variant report

Variant	rs13124352
Chromosome Location	chr4:69216264-69216265
allele	A/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	NRF1	chr4:69215380-69216272	SK-N-SH	brain:	n/a	n/a
2	MAZ	chr4:69214585-69216418	IMR90	lung:	n/a	n/a
3	MTA3	chr4:69215512-69216331	GM12878	blood:	n/a	n/a
4	REST	chr4:69214737-69216535	H1-neurons	neurons:	n/a	n/a
5	MAX	chr4:69215339-69216295	ECC-1	luminal epithelium:	n/a	n/a
6	MXI1	chr4:69213735-69216403	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:69215299-69216450	PFSK-1	brain:	n/a	n/a
8	CREB1	chr4:69215356-69216278	GM12878	blood:	n/a	chr4:69215895-69215908
9	IRF1	chr4:69215620-69216342	K562	blood:	n/a	chr4:69215859-69215873 chr4:69215867-69215881
10	SETDB1	chr4:69215664-69216413	K562	blood:	n/a	n/a
11	TAF1	chr4:69215244-69216312	ECC-1	luminal epithelium:	n/a	n/a
12	NR2F2	chr4:69215332-69216332	K562	blood:	n/a	n/a
13	MXI1	chr4:69214328-69216359	IMR90	lung:	n/a	n/a
14	JUN	chr4:69215416-69216292	K562	blood:	n/a	chr4:69215867-69215876 chr4:69215896-69215909 chr4:69215897-69215906
15	POLR2A	chr4:69215096-69216369	MCF-7	breast:	n/a	n/a
16	CREB1	chr4:69215301-69216326	K562	blood:	n/a	chr4:69215895-69215908
17	POLR2A	chr4:69215195-69216333	ProgFib	skin:	n/a	n/a
18	POLR2A	chr4:69214411-69216436	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOXA2	chr4:69215326-69216338	HepG2	liver:	n/a	n/a
20	MAX	chr4:69215372-69216291	HepG2	liver:	n/a	n/a
21	PML	chr4:69215359-69216269	GM12878	blood:	n/a	n/a
22	HA-E2F1	chr4:69215119-69216463	MCF-7	breast:	n/a	chr4:69215898-69215907 chr4:69215783-69215790 chr4:69215783-69215790 chr4:69215896-69215905 chr4:69215868-69215877 chr4:69215783-69215790
23	POLR2A	chr4:69214980-69216303	Raji	blood:	n/a	n/a
24	POLR2A	chr4:69215416-69216277	PFSK-1	brain:	n/a	n/a
25	SIN3AK20	chr4:69215187-69216329	MCF-7	breast:	n/a	n/a
26	CREB1	chr4:69215247-69216377	HepG2	liver:	n/a	chr4:69215895-69215908
27	HCFC1	chr4:69215165-69216328	K562	blood:	n/a	n/a
28	CTCF	chr4:69216212-69216276	Kidney_OC	kidney:	n/a	n/a
29	POLR2A	chr4:69215199-69216333	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr4:69214976-69216313	H1-hESC	embryonic stem cell:	n/a	n/a
31	MTA3	chr4:69215397-69216292	GM12878	blood:	n/a	n/a
32	CEBPB	chr4:69215567-69216276	MCF-7	breast:	n/a	chr4:69216013-69216024
33	POLR2A	chr4:69215255-69216506	HepG2	liver:	n/a	n/a
34	POLR2A	chr4:69215010-69216298	K562	blood:	n/a	n/a
35	POLR2A	chr4:69214349-69216525	GM12891	blood:	n/a	n/a
36	CBX3	chr4:69215467-69216389	K562	blood:	n/a	n/a
37	HCFC1	chr4:69215355-69216302	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45986990..45987747-chr4:69215457..69216399,2	Hela-S3	cervix:
2	chr4:69213512..69216500-chr4:69770884..69773457,2	MCF-7	breast:
3	chr4:69201801..69210708-chr4:69210917..69216982,18	MCF-7	breast:
4	chr21:45195495..45196196-chr4:69215418..69216293,2	Hela-S3	cervix:

Variant related genes	Relation type
YTHDC1	TF binding region
ENSG00000083896	Chromatin interaction
ENSG00000160213	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000272626	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10033058	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11726194	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727878	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13130430	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1406694	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17089267	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1715080	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1715081	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1730873	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1919898	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293595	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2319888	0.87[ASN][1000 genomes]
rs2319891	0.83[ASN][1000 genomes]
rs28656921	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34419508	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34452677	0.85[ASN][1000 genomes]
rs34500620	0.85[ASN][1000 genomes]
rs35632454	0.85[ASN][1000 genomes]
rs36098059	0.85[ASN][1000 genomes]
rs3797008	0.85[ASN][1000 genomes]
rs4428356	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4860929	0.85[ASN][1000 genomes]
rs57105149	0.82[ASN][1000 genomes]
rs57643586	0.81[ASN][1000 genomes]
rs58108365	0.81[ASN][1000 genomes]
rs62316045	0.81[ASN][1000 genomes]
rs6812178	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7666993	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv437385	chr4:69204755-69383357	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv437386	chr4:69213885-69383357	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13124352	YTHDC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69212200-69216400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:69212400-69216400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:69212600-69216400	Active TSS	Brain Germinal Matrix	brain
4	chr4:69212600-69216400	Active TSS	Fetal Kidney	kidney
5	chr4:69212800-69216400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr4:69213400-69216400	Active TSS	Colonic Mucosa	Colon
7	chr4:69213400-69216400	Active TSS	Stomach Smooth Muscle	stomach
8	chr4:69213600-69216400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:69213600-69216400	Active TSS	Fetal Brain Female	brain
10	chr4:69213600-69216400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr4:69213800-69216400	Active TSS	Muscle Satellite Cultured Cells	--
12	chr4:69213800-69216400	Active TSS	Brain Hippocampus Middle	brain
13	chr4:69213800-69216400	Active TSS	Colon Smooth Muscle	Colon
14	chr4:69214000-69216400	Active TSS	Duodenum Mucosa	Duodenum
15	chr4:69214000-69216400	Active TSS	Rectal Smooth Muscle	rectum
16	chr4:69214000-69216400	Active TSS	NHDF-Ad	bronchial
17	chr4:69214000-69216400	Active TSS	Osteobl	bone
18	chr4:69214200-69216400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:69214200-69216400	Active TSS	Liver	Liver
20	chr4:69214200-69216400	Active TSS	Brain Angular Gyrus	brain
21	chr4:69214200-69216400	Active TSS	Brain Cingulate Gyrus	brain
22	chr4:69214400-69216400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr4:69214600-69216400	Active TSS	Fetal Brain Male	brain
24	chr4:69214600-69216400	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr4:69215800-69216400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:69215800-69216400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:69215800-69216400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:69215800-69216400	Flanking Active TSS	Placenta	Placenta
29	chr4:69216000-69216400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:69216000-69216400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:69216000-69216400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:69216000-69216400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:69216000-69216400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr4:69216000-69216400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr4:69216000-69216400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
36	chr4:69216000-69216400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr4:69216000-69216400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr4:69216000-69216400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:69216000-69216400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:69216000-69216400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr4:69216000-69216400	Flanking Active TSS	Fetal Intestine Small	intestine
42	chr4:69216000-69216400	Flanking Active TSS	Fetal Lung	lung
43	chr4:69216000-69216400	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr4:69216000-69216400	Flanking Active TSS	Fetal Stomach	stomach
45	chr4:69216000-69216400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr4:69216000-69216400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr4:69216000-69216400	Enhancers	Spleen	Spleen
48	chr4:69216000-69216400	Flanking Active TSS	Dnd41	blood
49	chr4:69216000-69216400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr4:69216000-69219400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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