Variant report

Variant	rs1806652
Chromosome Location	chr12:57999101-57999102
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	POLR2A	chr12:57998690-57999323	U87	brain:	n/a	n/a
2	POLR2A	chr12:57998905-57999157	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:57998807-57999167	A549	lung:	n/a	n/a
4	POLR2A	chr12:57998780-57999213	SK-N-SH	brain:	n/a	n/a
5	ZBTB7A	chr12:57997906-57999285	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:57998716-57999467	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:57998155-57999228	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr12:57998878-57999109	A549	lung:	n/a	n/a
9	POLR2A	chr12:57998735-57999165	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr12:57998458-57999177	GM12892	blood:	n/a	n/a
11	YY1	chr12:57997896-57999282	SK-N-SH	brain:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
12	POLR2A	chr12:57998872-57999162	Gliobla	brain:	n/a	n/a
13	ZBTB7A	chr12:57997925-57999272	ECC-1	luminal epithelium:	n/a	n/a
14	TAF1	chr12:57998752-57999159	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:57998253-57999112	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr12:57998690-57999329	U87	brain:	n/a	n/a
17	POLR2A	chr12:57998707-57999103	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:57998800-57999150	H1-hESC	embryonic stem cell:	n/a	n/a
19	ELF1	chr12:57998703-57999212	GM12878	blood:	n/a	n/a
20	SIN3A	chr12:57998203-57999608	H1-hESC	embryonic stem cell:	n/a	chr12:57998248-57998257 chr12:57999287-57999295
21	MAZ	chr12:57997509-57999145	IMR90	lung:	n/a	chr12:57998373-57998383 chr12:57998608-57998617
22	MTA3	chr12:57998827-57999348	GM12878	blood:	n/a	n/a
23	TAF1	chr12:57998796-57999144	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr12:57998822-57999219	MCF-7	breast:	n/a	n/a
25	REST	chr12:57997829-57999536	H1-neurons	neurons:	n/a	chr12:57998955-57998965 chr12:57998491-57998500 chr12:57998494-57998507 chr12:57999285-57999294 chr12:57998393-57998402 chr12:57998302-57998312 chr12:57998248-57998258
26	POLR2A	chr12:57998213-57999274	ProgFib	skin:	n/a	n/a
27	POLR2A	chr12:57998725-57999138	GM12892	blood:	n/a	n/a
28	POLR2A	chr12:57998898-57999119	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr12:57998672-57999188	A549	lung:	n/a	n/a
30	POLR2A	chr12:57998275-57999196	MCF-7	breast:	n/a	n/a
31	POLR2A	chr12:57998788-57999130	MCF-7	breast:	n/a	n/a
32	TBP	chr12:57998213-57999269	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:57998849-57999121	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr12:57997942-57999324	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr12:57998877-57999200	U87	brain:	n/a	n/a
36	YY1	chr12:57998126-57999169	ECC-1	luminal epithelium:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
37	POLR2A	chr12:57998278-57999119	HepG2	liver:	n/a	n/a
38	YY1	chr12:57998075-57999328	SK-N-SH_RA	brain:	n/a	chr12:57999309-57999325 chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
39	YY1	chr12:57998108-57999156	H1-hESC	embryonic stem cell:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
40	HEY1	chr12:57998891-57999188	HepG2	liver:	n/a	n/a
41	POLR2A	chr12:57998102-57999124	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr12:57998781-57999198	ECC-1	luminal epithelium:	n/a	n/a
43	TAF1	chr12:57998018-57999318	ECC-1	luminal epithelium:	n/a	n/a
44	TAF1	chr12:57998727-57999233	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:57998708-57999183	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57998188..58000440-chr12:58014339..58016922,2	MCF-7	breast:
2	chr12:57824494..57826362-chr12:57997412..57999477,2	K562	blood:
3	chr12:57997608..58000545-chr12:58238111..58240464,2	MCF-7	breast:
4	chr12:57983454..57989400-chr12:57989791..58002327,29	MCF-7	breast:
5	chr12:57940405..57942301-chr12:57997757..58000737,2	MCF-7	breast:
6	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:
7	chr12:57997150..58000080-chr12:58158932..58161067,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF25	TF binding region
DTX3	TF binding region
ENSG00000135454	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10747780	0.82[CEU][hapmap];0.81[CHB][hapmap];0.83[TSI][hapmap]
rs11172262	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1545783	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2619439	0.86[EUR][1000 genomes]
rs34181394	0.85[EUR][1000 genomes]
rs4760158	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs60586224	0.87[EUR][1000 genomes]
rs71461330	0.90[EUR][1000 genomes]
rs7305391	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs7314872	0.89[EUR][1000 genomes]
rs7964896	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs812315	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8873	0.80[CEU][hapmap];0.81[GIH][hapmap];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer 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	96 gene(s)	inside rSNPs	diseases
2	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1806652	ARHGEF25	cis	Nerve Tibial	GTEx
rs1806652	AC025165.8	cis	Nerve Tibial	GTEx
rs1806652	ARHGEF25	cis	parietal	SCAN
rs1806652	PIP4K2C	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57993000-57999600	Weak transcription	K562	blood
2	chr12:57997400-57999200	Active TSS	Brain Anterior Caudate	brain
3	chr12:57997600-57999600	Active TSS	Colon Smooth Muscle	Colon
4	chr12:57997800-57999200	Active TSS	H9 Cell Line	embryonic stem cell
5	chr12:57997800-57999200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:57997800-57999400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:57997800-57999400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr12:57997800-57999400	Active TSS	Ovary	ovary
9	chr12:57997800-57999600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:57997800-57999600	Active TSS	Aorta	Aorta
11	chr12:57997800-57999800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr12:57998000-57999200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:57998000-57999200	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr12:57998000-57999200	Active TSS	Placenta Amnion	Placenta Amnion
15	chr12:57998000-57999200	Active TSS	Right Atrium	heart
16	chr12:57998000-57999200	Active TSS	NHLF	lung
17	chr12:57998000-57999400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr12:57998000-57999400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:57998000-57999400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:57998000-57999400	Active TSS	Colonic Mucosa	Colon
21	chr12:57998000-57999400	Flanking Active TSS	Dnd41	blood
22	chr12:57998000-57999600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:57998000-57999600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr12:57998000-57999600	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr12:57998000-57999800	Flanking Active TSS	Thymus	Thymus
26	chr12:57998200-57999200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:57998200-57999200	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr12:57998200-57999200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:57998200-57999200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:57998200-57999200	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:57998200-57999200	Active TSS	Brain Hippocampus Middle	brain
32	chr12:57998200-57999200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr12:57998200-57999200	Active TSS	Brain Substantia Nigra	brain
34	chr12:57998200-57999200	Flanking Active TSS	Esophagus	oesophagus
35	chr12:57998200-57999200	Active TSS	Fetal Lung	lung
36	chr12:57998200-57999200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr12:57998200-57999200	Active TSS	NHDF-Ad	bronchial
38	chr12:57998200-57999200	Active TSS	Osteobl	bone
39	chr12:57998200-57999400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:57998200-57999400	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr12:57998200-57999400	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:57998200-57999400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:57998200-57999400	Active TSS	Rectal Smooth Muscle	rectum
44	chr12:57998200-57999400	Active TSS	Small Intestine	intestine
45	chr12:57998200-57999600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr12:57998200-57999600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr12:57998200-57999600	Active TSS	Fetal Kidney	kidney
48	chr12:57998400-57999200	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr12:57998400-57999200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:57998400-57999200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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