Variant report

Variant	rs34181394
Chromosome Location	chr12:58005273-58005274
allele	C/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	EP300	chr12:58004970-58005284	K562	blood:	n/a	n/a
2	POLR2A	chr12:58004765-58005560	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:58004955-58005510	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:58004756-58005632	U87	brain:	n/a	n/a
5	POLR2A	chr12:58004862-58005500	GM19099	blood:	n/a	n/a
6	IRF1	chr12:58004934-58005443	K562	blood:	n/a	chr12:58005158-58005172 chr12:58005179-58005193
7	EGR1	chr12:58005233-58005521	K562	blood:	n/a	chr12:58005274-58005287 chr12:58005401-58005414
8	POLR2A	chr12:58004756-58005576	U87	brain:	n/a	n/a
9	POLR2A	chr12:58004997-58005387	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr12:58005081-58005431	HepG2	liver:	n/a	n/a
11	MAX	chr12:58004759-58005695	HepG2	liver:	n/a	chr12:58005549-58005559 chr12:58005577-58005587 chr12:58005016-58005026 chr12:58005375-58005385
12	SIN3AK20	chr12:58005164-58005474	K562	blood:	n/a	n/a
13	HEY1	chr12:58005101-58005439	HepG2	liver:	n/a	n/a
14	CTCF	chr12:58005160-58005310	HCM	heart:	n/a	n/a
15	POLR2A	chr12:58004974-58005478	U87	brain:	n/a	n/a
16	MAX	chr12:58004874-58005358	SK-N-SH	brain:	n/a	chr12:58005016-58005026
17	MAZ	chr12:58005040-58005639	HepG2	liver:	n/a	chr12:58005549-58005559 chr12:58005577-58005587 chr12:58005375-58005385
18	POLR2A	chr12:58005028-58005435	GM18526	blood:	n/a	n/a
19	MAX	chr12:58004860-58005405	SK-N-SH	brain:	n/a	chr12:58005016-58005026 chr12:58005375-58005385
20	ELF1	chr12:58005188-58005645	K562	blood:	n/a	chr12:58005313-58005325 chr12:58005505-58005514
21	POLR2A	chr12:58005119-58005371	K562	blood:	n/a	n/a
22	TCF12	chr12:58004836-58005588	A549	lung:	n/a	n/a
23	RCOR1	chr12:58004885-58005453	K562	blood:	n/a	n/a
24	REST	chr12:58004932-58005669	H1-neurons	neurons:	n/a	chr12:58005549-58005562 chr12:58005156-58005169 chr12:58005221-58005239
25	ZBTB7A	chr12:58005023-58005860	K562	blood:	n/a	n/a
26	HNF4A	chr12:58005195-58005590	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:58004979-58005477	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:58004901-58005531	PFSK-1	brain:	n/a	n/a
29	TCF12	chr12:58004670-58005549	ECC-1	luminal epithelium:	n/a	n/a
30	ZBTB7A	chr12:58004602-58006076	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr12:58005098-58005431	HUVEC	blood vessel:	n/a	n/a
32	HEY1	chr12:58004910-58005587	HepG2	liver:	n/a	chr12:58004993-58005008
33	MXI1	chr12:58004136-58006760	SK-N-SH	brain:	n/a	n/a
34	MAX	chr12:58004963-58005297	K562	blood:	n/a	chr12:58005016-58005026
35	CEBPD	chr12:58004985-58005704	HepG2	liver:	n/a	n/a
36	HEY1	chr12:58004988-58005564	K562	blood:	n/a	chr12:58004993-58005008
37	ZNF384	chr12:58005209-58005311	K562	blood:	n/a	n/a
38	TAF1	chr12:58004972-58005508	HepG2	liver:	n/a	n/a
39	MXI1	chr12:58005272-58005273	H1-hESC	embryonic stem cell:	n/a	n/a
40	E2F6	chr12:58004957-58005329	K562	blood:	n/a	chr12:58005116-58005128
41	POLR2A	chr12:58004979-58005426	A549	lung:	n/a	n/a
42	POLR2A	chr12:58004943-58005416	Gliobla	brain:	n/a	n/a
43	POLR2A	chr12:58005013-58005459	PANC-1	pancreas:	n/a	n/a
44	YY1	chr12:58005016-58005417	K562	blood:	n/a	chr12:58005032-58005043 chr12:58005199-58005208
45	POLR2A	chr12:58004810-58005646	HepG2	liver:	n/a	n/a
46	IRF1	chr12:58005125-58005401	K562	blood:	n/a	chr12:58005158-58005172 chr12:58005179-58005193
47	ZBTB7A	chr12:58004757-58005872	K562	blood:	n/a	n/a
48	POLR2A	chr12:58004970-58005537	ProgFib	skin:	n/a	n/a
49	POLR2A	chr12:58005009-58005444	H1-neurons	neurons:	n/a	n/a
50	CHD2	chr12:58004867-58005360	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58004618..58008024-chr12:58024930..58028098,5	MCF-7	breast:
2	chr12:57912257..57915408-chr12:58000825..58006358,4	K562	blood:
3	chr12:57930705..57935401-chr12:58001977..58005950,4	K562	blood:
4	chr12:57911699..57918406-chr12:58000825..58010019,18	K562	blood:
5	chr12:58002964..58008004-chr12:58117447..58122099,5	MCF-7	breast:
6	chr12:57938852..57941348-chr12:58005104..58006975,2	K562	blood:
7	chr12:58004396..58008788-chr12:58163385..58167140,4	MCF-7	breast:

Variant related genes	Relation type
ARHGEF25	TF binding region
ENSG00000255737	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000037897	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11172262	0.84[EUR][1000 genomes]
rs1806652	0.85[EUR][1000 genomes]
rs60586224	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7305391	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7314872	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7964896	0.81[EUR][1000 genomes]
rs812315	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers 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	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34181394	AC025165.8	cis	Nerve Tibial	GTEx
rs34181394	ARHGEF25	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58003000-58005800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:58003200-58005800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58003200-58005800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr12:58003400-58005800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr12:58003400-58006000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:58003400-58006000	Active TSS	Fetal Kidney	kidney
7	chr12:58003600-58006000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr12:58003600-58006000	Active TSS	Colon Smooth Muscle	Colon
9	chr12:58003600-58006000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
10	chr12:58003600-58006000	Active TSS	Ovary	ovary
11	chr12:58003800-58005400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr12:58003800-58005800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr12:58003800-58005800	Active TSS	Aorta	Aorta
14	chr12:58003800-58005800	Enhancers	Fetal Brain Male	brain
15	chr12:58003800-58005800	Active TSS	Right Atrium	heart
16	chr12:58003800-58006000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:58003800-58006400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:58003800-58006400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
19	chr12:58004000-58006400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr12:58004200-58005400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr12:58004200-58005400	Bivalent Enhancer	Liver	Liver
25	chr12:58004200-58005400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
26	chr12:58004200-58005400	Bivalent/Poised TSS	NHEK	skin
27	chr12:58004200-58005600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr12:58004200-58005600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr12:58004200-58005800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr12:58004200-58006000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:58004200-58006000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
32	chr12:58004200-58006000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:58004200-58006200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
34	chr12:58004200-58006400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:58004400-58005400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:58004400-58005600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
37	chr12:58004400-58005600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
38	chr12:58004400-58006000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:58004400-58006000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:58004400-58006000	Active TSS	Brain Substantia Nigra	brain
41	chr12:58004400-58006200	Active TSS	Brain Angular Gyrus	brain
42	chr12:58004400-58006200	Active TSS	Left Ventricle	heart
43	chr12:58004600-58005600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr12:58004600-58005600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:58004600-58005600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr12:58004600-58005800	Active TSS	Rectal Smooth Muscle	rectum
47	chr12:58004600-58005800	Active TSS	Stomach Smooth Muscle	stomach
48	chr12:58004600-58006000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:58004800-58005400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
50	chr12:58004800-58005400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood

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