Variant report

Variant	rs12370189
Chromosome Location	chr12:1772615-1772616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:1772179-1772631	A549	lung:	n/a	chr12:1772410-1772426 chr12:1772553-1772562 chr12:1772286-1772299
2	E2F6	chr12:1771891-1772624	A549	lung:	n/a	n/a
3	MAX	chr12:1771900-1772828	HCT-116	colon:	n/a	n/a
4	CTBP2	chr12:1771902-1772782	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr12:1771968-1772821	A549	lung:	n/a	chr12:1772410-1772426 chr12:1772553-1772562 chr12:1772286-1772299
6	CTCF	chr12:1772156-1772617	H1-hESC	embryonic stem cell:	n/a	chr12:1772410-1772426 chr12:1772553-1772562 chr12:1772286-1772299
7	ZNF143	chr12:1771937-1772769	H1-hESC	embryonic stem cell:	n/a	chr12:1772250-1772269
8	EGR1	chr12:1771844-1772617	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr12:1771816-1772885	A549	lung:	n/a	n/a
10	CBX3	chr12:1772322-1772813	K562	blood:	n/a	n/a
11	GTF2F1	chr12:1771905-1772625	H1-hESC	embryonic stem cell:	n/a	n/a
12	ZNF143	chr12:1772249-1772852	K562	blood:	n/a	chr12:1772250-1772269
13	MAX	chr12:1771841-1772682	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF2	chr12:1772353-1772871	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr12:1771870-1772710	H1-hESC	embryonic stem cell:	n/a	chr12:1772033-1772047
16	KAP1	chr12:1772280-1772860	HEK293	kidney:	n/a	n/a
17	TBP	chr12:1771946-1772777	K562	blood:	n/a	n/a
18	CTCF	chr12:1772134-1772688	K562	blood:	n/a	chr12:1772410-1772426 chr12:1772553-1772562 chr12:1772286-1772299
19	CREB1	chr12:1772288-1772665	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr12:1772600-1772750	AG04449	skin:	n/a	n/a
21	CBX3	chr12:1771902-1772778	K562	blood:	n/a	n/a
22	MAX	chr12:1771883-1772788	A549	lung:	n/a	n/a
23	MAX	chr12:1771897-1772655	K562	blood:	n/a	n/a
24	MAX	chr12:1772028-1772668	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr12:1771858-1772700	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F6	chr12:1771879-1772709	H1-hESC	embryonic stem cell:	n/a	n/a
27	EGR1	chr12:1771826-1772620	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr12:1772170-1772734	HepG2	liver:	n/a	n/a
29	TEAD4	chr12:1772270-1772617	K562	blood:	n/a	n/a
30	MAX	chr12:1771927-1772729	A549	lung:	n/a	n/a
31	CTCF	chr12:1772192-1772626	H1-hESC	embryonic stem cell:	n/a	chr12:1772410-1772426 chr12:1772553-1772562 chr12:1772286-1772299

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:1771146..1773921-chr12:1806258..1810268,3	K562	blood:
2	chr12:1770841..1772886-chr12:1868633..1870687,2	K562	blood:
3	chr12:1713956..1716010-chr12:1769729..1772627,2	K562	blood:
4	chr12:1768367..1774746-chr12:1797764..1801789,11	MCF-7	breast:
5	chr12:1769759..1773174-chr12:1808605..1811319,4	K562	blood:
6	chr12:1772017..1774771-chr12:1791247..1793999,2	K562	blood:
7	chr12:1769387..1773191-chr12:1797591..1801415,7	K562	blood:
8	chr12:1769849..1773599-chr12:1775643..1780093,7	K562	blood:
9	chr12:1771225..1773425-chr12:1825793..1828213,2	K562	blood:
10	chr12:1770828..1772628-chr12:1803369..1805414,2	MCF-7	breast:
11	chr12:1770529..1774414-chr12:1775801..1779567,5	K562	blood:
12	chr12:1771041..1773403-chr12:1779231..1780739,2	MCF-7	breast:
13	chr12:1772246..1773869-chr12:1801718..1803350,2	MCF-7	breast:
14	chr12:1751543..1753813-chr12:1771357..1773090,2	K562	blood:
15	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:
16	chr12:1770836..1772849-chr12:1788601..1790387,2	K562	blood:
17	chr12:1770854..1772922-chr12:1803554..1806296,3	MCF-7	breast:
18	chr12:1771124..1772646-chr12:1920146..1921808,2	K562	blood:

No data

Variant related genes	Relation type
MIR3649	TF binding region
ENSG00000006831	Chromatin interaction
ENSG00000271500	Chromatin interaction
ENSG00000151062	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10734999	0.85[CHB][hapmap]
rs10744548	0.85[CHB][hapmap]
rs10773979	0.85[CHB][hapmap]
rs10848554	0.85[CHB][hapmap]
rs10848568	0.85[CHB][hapmap]
rs11836547	0.85[CHB][hapmap]
rs12814301	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4140993	0.85[CHB][hapmap]
rs7134070	0.85[CHB][hapmap]
rs7138701	0.85[CHB][hapmap]
rs7302234	0.85[CHB][hapmap]
rs7311218	0.82[CHB][hapmap]
rs7488369	0.85[CHB][hapmap]
rs767870	0.85[CHB][hapmap]
rs9805042	0.85[CHB][hapmap]

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	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3344009	chr12:1770516-1773064	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3341098	chr12:1770566-1773039	Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12370189	NCF4	trans	lymphoblastoid	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1770000-1772800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:1770000-1774000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:1770200-1774400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr12:1770800-1773200	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:1771000-1775400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:1771400-1772800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr12:1771400-1774000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:1771400-1774000	Weak transcription	Primary T cells from cord blood	blood
9	chr12:1771400-1774000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:1771400-1774000	Weak transcription	Hela-S3	cervix
11	chr12:1771400-1774200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:1771400-1774200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:1771400-1774200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:1771400-1775200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:1771400-1775800	Weak transcription	Brain Angular Gyrus	brain
16	chr12:1771400-1775800	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:1771400-1775800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:1771400-1776000	Weak transcription	Brain Anterior Caudate	brain
19	chr12:1771400-1776000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:1771400-1777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:1771400-1777800	Weak transcription	GM12878-XiMat	blood
22	chr12:1771600-1772800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:1771600-1773800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:1771600-1774200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:1771600-1774200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:1771600-1774200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr12:1771600-1774400	Weak transcription	Thymus	Thymus
28	chr12:1771600-1775400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:1771600-1775400	Weak transcription	Dnd41	blood
30	chr12:1771600-1776000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:1771600-1776000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:1771600-1776000	Weak transcription	Ovary	ovary
33	chr12:1771600-1778000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:1772000-1772800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:1772200-1772800	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:1772200-1772800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
37	chr12:1772200-1772800	Bivalent Enhancer	Placenta	Placenta
38	chr12:1772200-1772800	Enhancers	Spleen	Spleen
39	chr12:1772200-1773200	Weak transcription	Adipose Nuclei	Adipose
40	chr12:1772200-1774800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr12:1772200-1776200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr12:1772200-1778000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:1772400-1772800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
44	chr12:1772400-1772800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
45	chr12:1772400-1772800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
46	chr12:1772400-1772800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr12:1772400-1772800	Flanking Active TSS	Brain Substantia Nigra	brain
48	chr12:1772400-1772800	Flanking Active TSS	A549	lung
49	chr12:1772400-1772800	Enhancers	HepG2	liver
50	chr12:1772400-1772800	Flanking Active TSS	K562	blood

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