Variant report

Variant	rs71461330
Chromosome Location	chr12:57998722-57998723
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	POLR2A	chr12:57998690-57999323	U87	brain:	n/a	n/a
2	MAX	chr12:57998246-57999028	ECC-1	luminal epithelium:	n/a	chr12:57998373-57998383 chr12:57998608-57998617
3	USF1	chr12:57998132-57998900	SK-N-SH	brain:	n/a	chr12:57998862-57998878 chr12:57998756-57998772
4	YY1	chr12:57998149-57998723	A549	lung:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
5	CTCF	chr12:57998680-57998830	AG04449	skin:	n/a	n/a
6	USF1	chr12:57998264-57998782	A549	lung:	n/a	chr12:57998756-57998772
7	USF1	chr12:57998223-57999027	ECC-1	luminal epithelium:	n/a	chr12:57998862-57998878 chr12:57998756-57998772
8	USF1	chr12:57998257-57998965	SK-N-SH_RA	brain:	n/a	chr12:57998862-57998878 chr12:57998756-57998772
9	USF1	chr12:57998344-57998748	A549	lung:	n/a	n/a
10	YY1	chr12:57998045-57998786	SK-N-SH	brain:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
11	ZBTB7A	chr12:57997906-57999285	ECC-1	luminal epithelium:	n/a	n/a
12	USF1	chr12:57998142-57998996	H1-hESC	embryonic stem cell:	n/a	chr12:57998862-57998878 chr12:57998756-57998772
13	POLR2A	chr12:57998716-57999467	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr12:57998155-57999228	H1-neurons	neurons:	n/a	n/a
15	YY1	chr12:57998167-57998959	GM12878	blood:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
16	YY1	chr12:57998218-57998859	NT2-D1	testis:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
17	YY1	chr12:57998146-57999061	GM12892	blood:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
18	POLR2A	chr12:57998458-57999177	GM12892	blood:	n/a	n/a
19	YY1	chr12:57997896-57999282	SK-N-SH	brain:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
20	ZBTB7A	chr12:57997925-57999272	ECC-1	luminal epithelium:	n/a	n/a
21	YY1	chr12:57998085-57999060	SK-N-SH_RA	brain:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
22	POLR2A	chr12:57998253-57999112	HUVEC	blood vessel:	n/a	n/a
23	USF1	chr12:57998281-57998790	A549	lung:	n/a	chr12:57998756-57998772
24	POLR2A	chr12:57998690-57999329	U87	brain:	n/a	n/a
25	POLR2A	chr12:57997384-57998734	MCF-7	breast:	n/a	n/a
26	USF1	chr12:57998116-57999077	ECC-1	luminal epithelium:	n/a	chr12:57998862-57998878 chr12:57998756-57998772
27	POLR2A	chr12:57998707-57999103	GM12878	blood:	n/a	n/a
28	USF2	chr12:57998336-57998761	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr12:57998235-57999082	HepG2	liver:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
30	YY1	chr12:57998104-57999022	GM12878	blood:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
31	POLR2A	chr12:57998204-57998890	H1-hESC	embryonic stem cell:	n/a	n/a
32	ELF1	chr12:57998703-57999212	GM12878	blood:	n/a	n/a
33	SIN3A	chr12:57998203-57999608	H1-hESC	embryonic stem cell:	n/a	chr12:57998248-57998257 chr12:57999287-57999295
34	MAZ	chr12:57997509-57999145	IMR90	lung:	n/a	chr12:57998373-57998383 chr12:57998608-57998617
35	POLR2A	chr12:57998001-57998752	GM12892	blood:	n/a	n/a
36	MTA3	chr12:57998081-57998772	GM12878	blood:	n/a	n/a
37	YY1	chr12:57997577-57999098	ECC-1	luminal epithelium:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
38	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
39	POLR2A	chr12:57998213-57999274	ProgFib	skin:	n/a	n/a
40	TCF12	chr12:57998672-57999188	A549	lung:	n/a	n/a
41	POLR2A	chr12:57998275-57999196	MCF-7	breast:	n/a	n/a
42	TBP	chr12:57998213-57999269	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:57997942-57999324	H1-hESC	embryonic stem cell:	n/a	n/a
44	CREB1	chr12:57998273-57998739	GM12878	blood:	n/a	chr12:57998362-57998375
45	POLR2A	chr12:57998286-57998821	Gliobla	brain:	n/a	n/a
46	USF1	chr12:57998237-57999041	SK-N-SH	brain:	n/a	chr12:57998862-57998878 chr12:57998756-57998772
47	YY1	chr12:57998126-57999169	ECC-1	luminal epithelium:	n/a	chr12:57998620-57998630 chr12:57998399-57998411 chr12:57998400-57998422 chr12:57998400-57998410
48	USF1	chr12:57998348-57998823	SK-N-SH_RA	brain:	n/a	chr12:57998756-57998772
49	TAF1	chr12:57998716-57998934	GM12878	blood:	n/a	n/a
50	TAF1	chr12:57998163-57998870	H1-neurons	neurons:	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	chr12:57913753..57916510-chr12:57996799..57998980,2	MCF-7	breast:
4	chr12:57997608..58000545-chr12:58238111..58240464,2	MCF-7	breast:
5	chr12:57983454..57989400-chr12:57989791..58002327,29	MCF-7	breast:
6	chr12:57940405..57942301-chr12:57997757..58000737,2	MCF-7	breast:
7	chr12:57997114..58001112-chr12:58025485..58030490,5	MCF-7	breast:
8	chr12:57997150..58000080-chr12:58158932..58161067,2	MCF-7	breast:

Variant related genes	Relation type
DTX3	TF binding region
ENSG00000175203	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000179912	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000258001	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11172262	0.87[EUR][1000 genomes]
rs1806652	0.90[EUR][1000 genomes]
rs2619439	0.80[EUR][1000 genomes]
rs60586224	0.81[EUR][1000 genomes]
rs7314872	0.81[EUR][1000 genomes]
rs7964896	0.86[EUR][1000 genomes]
rs812315	0.87[EUR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57993000-57999600	Weak transcription	K562	blood
2	chr12:57997400-57998800	Enhancers	HMEC	breast
3	chr12:57997400-57999200	Active TSS	Brain Anterior Caudate	brain
4	chr12:57997600-57999000	Active TSS	Fetal Brain Female	brain
5	chr12:57997600-57999600	Active TSS	Colon Smooth Muscle	Colon
6	chr12:57997800-57998800	Enhancers	Spleen	Spleen
7	chr12:57997800-57999000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr12:57997800-57999200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:57997800-57999200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:57997800-57999400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:57997800-57999400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr12:57997800-57999400	Active TSS	Ovary	ovary
13	chr12:57997800-57999600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:57997800-57999600	Active TSS	Aorta	Aorta
15	chr12:57997800-57999800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:57998000-57998800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:57998000-57999000	Active TSS	Brain Angular Gyrus	brain
18	chr12:57998000-57999200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr12:57998000-57999200	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:57998000-57999200	Active TSS	Placenta Amnion	Placenta Amnion
21	chr12:57998000-57999200	Active TSS	Right Atrium	heart
22	chr12:57998000-57999200	Active TSS	NHLF	lung
23	chr12:57998000-57999400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr12:57998000-57999400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:57998000-57999400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:57998000-57999400	Active TSS	Colonic Mucosa	Colon
27	chr12:57998000-57999400	Flanking Active TSS	Dnd41	blood
28	chr12:57998000-57999600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:57998000-57999600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr12:57998000-57999600	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr12:57998000-57999800	Flanking Active TSS	Thymus	Thymus
32	chr12:57998200-57998800	Active TSS	Right Ventricle	heart
33	chr12:57998200-57999000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:57998200-57999000	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
35	chr12:57998200-57999000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:57998200-57999000	Active TSS	Fetal Heart	heart
37	chr12:57998200-57999000	Bivalent/Poised TSS	Fetal Stomach	stomach
38	chr12:57998200-57999200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:57998200-57999200	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr12:57998200-57999200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:57998200-57999200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:57998200-57999200	Active TSS	Brain Cingulate Gyrus	brain
43	chr12:57998200-57999200	Active TSS	Brain Hippocampus Middle	brain
44	chr12:57998200-57999200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr12:57998200-57999200	Active TSS	Brain Substantia Nigra	brain
46	chr12:57998200-57999200	Flanking Active TSS	Esophagus	oesophagus
47	chr12:57998200-57999200	Active TSS	Fetal Lung	lung
48	chr12:57998200-57999200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
49	chr12:57998200-57999200	Active TSS	NHDF-Ad	bronchial
50	chr12:57998200-57999200	Active TSS	Osteobl	bone

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