Variant report

Variant	rs34399241
Chromosome Location	chr12:57607483-57607484
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	MYC	chr12:57607087-57607550	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr12:57606989-57607968	ECC-1	luminal epithelium:	n/a	n/a
3	RAD21	chr12:57606956-57607515	H1-hESC	embryonic stem cell:	n/a	chr12:57607252-57607265 chr12:57607341-57607353 chr12:57607236-57607255
4	POLR2A	chr12:57606903-57610506	U87	brain:	n/a	n/a
5	CTBP2	chr12:57607083-57608538	H1-hESC	embryonic stem cell:	n/a	n/a
6	TCF12	chr12:57607124-57608551	ECC-1	luminal epithelium:	n/a	chr12:57608410-57608420 chr12:57607780-57607788 chr12:57607687-57607694
7	POLR2A	chr12:57607156-57608345	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:57607153-57610401	U87	brain:	n/a	n/a
9	ZKSCAN1	chr12:57607184-57607486	Hela-S3	cervix:	n/a	n/a
10	FOXM1	chr12:57606953-57607544	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:57607125-57608981	HepG2	liver:	n/a	n/a
12	CTCF	chr12:57607440-57607590	GM12873	blood:	n/a	n/a
13	BCL3	chr12:57607082-57608396	A549	lung:	n/a	n/a
14	ZNF263	chr12:57607203-57608472	HEK293-T-REx	kidney:	n/a	chr12:57608126-57608147 chr12:57608100-57608121 chr12:57608003-57608012
15	RAD21	chr12:57607028-57607574	IMR90	lung:	n/a	chr12:57607252-57607265 chr12:57607341-57607353 chr12:57607236-57607255
16	YY1	chr12:57607168-57607551	ECC-1	luminal epithelium:	n/a	n/a
17	MAX	chr12:57606990-57607584	A549	lung:	n/a	n/a
18	MAX	chr12:57607015-57607902	ECC-1	luminal epithelium:	n/a	n/a
19	HA-E2F1	chr12:57607045-57607660	MCF-7	breast:	n/a	n/a
20	RAD21	chr12:57607088-57607563	A549	lung:	n/a	chr12:57607252-57607265 chr12:57607341-57607353 chr12:57607236-57607255
21	MXI1	chr12:57606959-57607589	IMR90	lung:	n/a	n/a
22	SIN3A	chr12:57607127-57607681	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr12:57607145-57608931	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr12:57607241-57609488	HepG2	liver:	n/a	n/a
25	CTCF	chr12:57607005-57607517	MCF-7	breast:	n/a	chr12:57607238-57607247 chr12:57607235-57607253 chr12:57607237-57607258
26	E2F6	chr12:57606982-57607566	A549	lung:	n/a	n/a
27	SMC3	chr12:57606739-57607883	SK-N-SH	brain:	n/a	chr12:57607237-57607244 chr12:57607237-57607251
28	POLR2A	chr12:57606909-57610500	U87	brain:	n/a	n/a
29	CTCF	chr12:57606897-57607631	HCT-116	colon:	n/a	chr12:57607238-57607247 chr12:57607235-57607253 chr12:57607237-57607258
30	CTCF	chr12:57606973-57607489	A549	lung:	n/a	chr12:57607238-57607247 chr12:57607235-57607253 chr12:57607237-57607258
31	RAD21	chr12:57606935-57608753	HCT-116	colon:	n/a	chr12:57608252-57608271 chr12:57607747-57607761 chr12:57608253-57608267 chr12:57607252-57607265 chr12:57608253-57608262 chr12:57607341-57607353 chr12:57608632-57608651 chr12:57607236-57607255 chr12:57608637-57608647
32	RFX5	chr12:57606888-57610516	IMR90	lung:	n/a	chr12:57609655-57609664 chr12:57609652-57609667 chr12:57609653-57609667
33	RAD21	chr12:57606725-57607703	SK-N-SH	brain:	n/a	chr12:57607252-57607265 chr12:57607341-57607353 chr12:57607236-57607255
34	MAX	chr12:57607010-57607873	MCF-7	breast:	n/a	n/a
35	CTCF	chr12:57606638-57608714	A549	lung:	n/a	chr12:57608634-57608647 chr12:57608636-57608646 chr12:57608254-57608263 chr12:57608631-57608649 chr12:57608633-57608654 chr12:57607238-57607247 chr12:57607235-57607253 chr12:57608251-57608269 chr12:57607237-57607258 chr12:57608252-57608268 chr12:57608634-57608643
36	MAX	chr12:57607077-57607534	SK-N-SH	brain:	n/a	n/a
37	RAD21	chr12:57606985-57607621	A549	lung:	n/a	chr12:57607252-57607265 chr12:57607341-57607353 chr12:57607236-57607255
38	BHLHE40	chr12:57607104-57607604	K562	blood:	n/a	n/a
39	FOSL2	chr12:57607050-57608658	HepG2	liver:	n/a	n/a
40	MAX	chr12:57606937-57607598	MCF-7	breast:	n/a	n/a
41	CTCF	chr12:57606993-57607572	MCF-7	breast:	n/a	chr12:57607238-57607247 chr12:57607235-57607253 chr12:57607237-57607258
42	MAX	chr12:57607153-57607511	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr12:57607151-57607516	HCT-116	colon:	n/a	n/a
44	CTCF	chr12:57606645-57608913	HCT-116	colon:	n/a	chr12:57608634-57608647 chr12:57608636-57608646 chr12:57608254-57608263 chr12:57608631-57608649 chr12:57608633-57608654 chr12:57607238-57607247 chr12:57607235-57607253 chr12:57608251-57608269 chr12:57607237-57607258 chr12:57608252-57608268 chr12:57608634-57608643
45	CTCF	chr12:57607440-57607590	GM12869	blood:	n/a	n/a
46	MAX	chr12:57607125-57607486	SK-N-SH	brain:	n/a	n/a
47	CTCF	chr12:57607440-57607590	GM12875	blood:	n/a	n/a
48	MAX	chr12:57607020-57607569	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr12:57606279-57609127	SK-N-SH	brain:	n/a	chr12:57608634-57608647 chr12:57608636-57608646 chr12:57608254-57608263 chr12:57608631-57608649 chr12:57608633-57608654 chr12:57607238-57607247 chr12:57607235-57607253 chr12:57608251-57608269 chr12:57607237-57607258 chr12:57608252-57608268 chr12:57608634-57608643
50	POLR2A	chr12:57607468-57607622	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57586695..57588801-chr12:57605847..57608117,2	MCF-7	breast:
2	chr12:57480154..57482467-chr12:57605881..57608725,2	K562	blood:
3	chr12:57606014..57610025-chr12:57631623..57633806,36	MCF-7	breast:
4	chr12:57606643..57608087-chr12:57636460..57637985,5	MCF-7	breast:
5	chr12:57606792..57609175-chr12:57630908..57633525,50	K562	blood:
6	chr12:57607441..57608995-chr12:57610521..57612256,2	MCF-7	breast:
7	chr12:57606818..57608471-chr12:57912067..57913671,2	K562	blood:
8	chr12:57588577..57592670-chr12:57606671..57608811,3	K562	blood:
9	chr12:57588577..57590373-chr12:57606431..57608754,2	K562	blood:
10	chr12:57606805..57607594-chr12:57628764..57629987,3	K562	blood:
11	chr12:57531973..57533574-chr12:57605011..57607679,2	MCF-7	breast:
12	chr12:57606546..57610160-chr12:57612220..57614034,3	K562	blood:
13	chr12:57606466..57609055-chr12:57636459..57638396,24	K562	blood:
14	chr12:57598445..57603565-chr12:57603905..57607963,7	K562	blood:
15	chr12:57578786..57581016-chr12:57606054..57608817,2	MCF-7	breast:
16	chr12:57606205..57609184-chr12:57636393..57638193,29	MCF-7	breast:
17	chr12:57607171..57607774-chr12:57846242..57847293,3	K562	blood:
18	chr12:57607241..57608791-chr12:57610365..57612075,2	K562	blood:

Variant related genes	Relation type
NXPH4	TF binding region
ENSG00000221365	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000182379	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs34185879	0.88[AFR][1000 genomes]
rs34849929	0.88[AFR][1000 genomes]
rs7485650	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7977876	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv869636	chr12:57590172-57613714	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57585800-57608600	Strong transcription	NHLF	lung
2	chr12:57601800-57608000	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr12:57603200-57610200	Weak transcription	Right Atrium	heart
4	chr12:57604800-57608200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:57604800-57608200	Genic enhancers	HSMM	muscle
6	chr12:57605400-57607800	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr12:57605600-57608000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:57605800-57609400	Weak transcription	Lung	lung
9	chr12:57606000-57608000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:57606000-57608400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:57606200-57608000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:57606400-57608000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:57606400-57610200	Weak transcription	Aorta	Aorta
14	chr12:57606600-57607800	Weak transcription	HepG2	liver
15	chr12:57606600-57608000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:57606600-57608000	Weak transcription	Esophagus	oesophagus
17	chr12:57606600-57608200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:57606600-57608400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:57606600-57608600	Enhancers	Fetal Brain Male	brain
20	chr12:57606600-57608600	Enhancers	Left Ventricle	heart
21	chr12:57606800-57607600	Weak transcription	Colonic Mucosa	Colon
22	chr12:57606800-57607600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:57606800-57607600	Enhancers	Stomach Mucosa	stomach
24	chr12:57606800-57607800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:57606800-57607800	Genic enhancers	Adipose Nuclei	Adipose
26	chr12:57606800-57607800	Genic enhancers	Brain Hippocampus Middle	brain
27	chr12:57606800-57607800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:57606800-57607800	Genic enhancers	Fetal Brain Female	brain
29	chr12:57606800-57608000	Genic enhancers	Fetal Stomach	stomach
30	chr12:57606800-57608000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:57606800-57608200	Genic enhancers	Osteobl	bone
32	chr12:57606800-57608400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr12:57606800-57608400	Enhancers	Placenta	Placenta
34	chr12:57606800-57608600	Enhancers	A549	lung
35	chr12:57606800-57609000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:57606800-57609400	Weak transcription	Gastric	stomach
37	chr12:57606800-57609600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
38	chr12:57606800-57609600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:57606800-57609600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:57606800-57609800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr12:57606800-57610200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
42	chr12:57606800-57610200	Enhancers	Pancreas	Pancrea
43	chr12:57607000-57607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:57607000-57608200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
45	chr12:57607000-57609200	Weak transcription	Liver	Liver
46	chr12:57607000-57609800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:57607200-57607600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:57607200-57607600	Enhancers	Ovary	ovary
49	chr12:57607200-57607600	Enhancers	Stomach Smooth Muscle	stomach
50	chr12:57607200-57607600	Flanking Active TSS	Dnd41	blood

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