Variant report

Variant	rs4941653
Chromosome Location	chr13:50200008-50200009
allele	C/T
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	MAFK	chr13:50199799-50200200	H1-hESC	embryonic stem cell:	n/a	chr13:50199987-50199996 chr13:50199986-50200000 chr13:50199983-50200003 chr13:50199988-50200003 chr13:50199990-50199999 chr13:50199989-50199999 chr13:50199985-50200001
2	MAFK	chr13:50199592-50200357	HepG2	liver:	n/a	chr13:50199987-50199996 chr13:50199986-50200000 chr13:50199983-50200003 chr13:50199988-50200003 chr13:50199990-50199999 chr13:50199989-50199999 chr13:50199985-50200001
3	MAFF	chr13:50199532-50200450	HepG2	liver:	n/a	chr13:50199986-50200000 chr13:50199980-50199998
4	NR2C2	chr13:50199526-50200076	Hela-S3	cervix:	n/a	chr13:50199749-50199762
5	CHD2	chr13:50199566-50200078	HepG2	liver:	n/a	n/a
6	POLR2A	chr13:50199434-50200054	HepG2	liver:	n/a	n/a
7	MAFK	chr13:50199495-50200456	HepG2	liver:	n/a	chr13:50199987-50199996 chr13:50199986-50200000 chr13:50199983-50200003 chr13:50199988-50200003 chr13:50199990-50199999 chr13:50199989-50199999 chr13:50199985-50200001
8	POLR2A	chr13:50199475-50200070	HepG2	liver:	n/a	n/a
9	EP300	chr13:50199513-50200067	HepG2	liver:	n/a	n/a
10	MAFK	chr13:50199747-50200374	IMR90	lung:	n/a	chr13:50199987-50199996 chr13:50199986-50200000 chr13:50199983-50200003 chr13:50199988-50200003 chr13:50199990-50199999 chr13:50199989-50199999 chr13:50199985-50200001
11	MAZ	chr13:50199583-50200117	Hela-S3	cervix:	n/a	n/a
12	MAFK	chr13:50199807-50200186	K562	blood:	n/a	chr13:50199987-50199996 chr13:50199986-50200000 chr13:50199983-50200003 chr13:50199988-50200003 chr13:50199990-50199999 chr13:50199989-50199999 chr13:50199985-50200001
13	MXI1	chr13:50199484-50200467	HepG2	liver:	n/a	n/a
14	MYC	chr13:50199258-50200051	Hela-S3	cervix:	n/a	chr13:50199685-50199695
15	YY1	chr13:50199453-50200053	HepG2	liver:	n/a	n/a
16	MAX	chr13:50199110-50200397	HepG2	liver:	n/a	chr13:50199685-50199695
17	RFX5	chr13:50199745-50200337	HepG2	liver:	n/a	n/a
18	MAFK	chr13:50199724-50200338	GM12878	blood:	n/a	chr13:50199987-50199996 chr13:50199986-50200000 chr13:50199983-50200003 chr13:50199988-50200003 chr13:50199990-50199999 chr13:50199989-50199999 chr13:50199985-50200001
19	MAX	chr13:50199251-50200278	HepG2	liver:	n/a	chr13:50199685-50199695
20	RFX5	chr13:50199612-50200121	Hela-S3	cervix:	n/a	n/a
21	MAFK	chr13:50199577-50200297	Hela-S3	cervix:	n/a	chr13:50199987-50199996 chr13:50199986-50200000 chr13:50199983-50200003 chr13:50199988-50200003 chr13:50199990-50199999 chr13:50199989-50199999 chr13:50199985-50200001
22	NR2F2	chr13:50199449-50200033	MCF-7	breast:	n/a	n/a
23	POLR2A	chr13:50199300-50200449	HepG2	liver:	n/a	n/a
24	MAFF	chr13:50199811-50200313	K562	blood:	n/a	chr13:50199986-50200000 chr13:50199980-50199998

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50198466..50201359-chr13:50202667..50205096,2	MCF-7	breast:
2	chr13:50016671..50019335-chr13:50197753..50200555,2	K562	blood:

Variant related genes	Relation type
ARL11	TF binding region
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs7140087	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7320206	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7986690	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer 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
4	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4941653	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50194600-50202000	Weak transcription	Esophagus	oesophagus
2	chr13:50194800-50201800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr13:50194800-50202000	Weak transcription	Primary B cells from cord blood	blood
4	chr13:50194800-50202000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr13:50194800-50202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr13:50194800-50202000	Weak transcription	Fetal Thymus	thymus
7	chr13:50194800-50202000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr13:50194800-50202200	Weak transcription	Colonic Mucosa	Colon
9	chr13:50194800-50202200	Weak transcription	K562	blood
10	chr13:50195800-50200400	Enhancers	Fetal Heart	heart
11	chr13:50197000-50201800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:50198600-50200400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr13:50198800-50200200	Enhancers	Lung	lung
14	chr13:50198800-50200400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:50198800-50200400	Enhancers	Spleen	Spleen
16	chr13:50199000-50201400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr13:50199200-50200200	Enhancers	Placenta	Placenta
18	chr13:50199200-50200400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:50199200-50200400	Enhancers	Fetal Intestine Large	intestine
20	chr13:50199200-50200800	Flanking Active TSS	HepG2	liver
21	chr13:50199400-50200200	Enhancers	Fetal Intestine Small	intestine
22	chr13:50199400-50200200	Enhancers	Fetal Muscle Trunk	muscle
23	chr13:50199400-50200400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr13:50199400-50200400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr13:50199400-50200400	Enhancers	Adipose Nuclei	Adipose
26	chr13:50199400-50200400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr13:50199400-50200400	Enhancers	Stomach Mucosa	stomach
28	chr13:50199400-50200400	Enhancers	NHDF-Ad	bronchial
29	chr13:50199600-50200200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:50199600-50200200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr13:50199600-50200200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:50199600-50200200	Enhancers	Brain Hippocampus Middle	brain
33	chr13:50199600-50200200	Enhancers	Pancreas	Pancrea
34	chr13:50199600-50200200	Enhancers	Right Atrium	heart
35	chr13:50199600-50200200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr13:50199600-50200400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr13:50199600-50200400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:50199600-50200400	Enhancers	Fetal Lung	lung
39	chr13:50199600-50200400	Enhancers	Ovary	ovary
40	chr13:50199600-50200600	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr13:50199600-50201200	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr13:50199800-50200200	Weak transcription	Gastric	stomach
43	chr13:50199800-50200200	Enhancers	HSMMtube	muscle
44	chr13:50199800-50200400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr13:50199800-50200400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:50199800-50200400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr13:50199800-50200400	Flanking Active TSS	Liver	Liver
48	chr13:50199800-50200400	Enhancers	Brain Substantia Nigra	brain
49	chr13:50199800-50200400	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr13:50199800-50202000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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