Variant report

Variant	rs73417632
Chromosome Location	chr12:122500941-122500942
allele	G/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	FOXA2	chr12:122500664-122501430	A549	lung:	n/a	n/a
2	MAFK	chr12:122500851-122501276	IMR90	lung:	n/a	n/a
3	GABPA	chr12:122500689-122501657	A549	lung:	n/a	n/a
4	SIN3AK20	chr12:122500779-122501711	MCF-7	breast:	n/a	n/a
5	TCF12	chr12:122500478-122503084	A549	lung:	n/a	chr12:122501076-122501085
6	NR3C1	chr12:122500662-122501290	A549	lung:	n/a	n/a
7	FOXA1	chr12:122500803-122501236	HepG2	liver:	n/a	n/a
8	POLR2A	chr12:122500717-122503319	PFSK-1	brain:	n/a	n/a
9	NR2F2	chr12:122500499-122502388	MCF-7	breast:	n/a	n/a
10	JUND	chr12:122500675-122501613	A549	lung:	n/a	chr12:122501405-122501413 chr12:122501406-122501417 chr12:122501403-122501415 chr12:122501405-122501412
11	MAX	chr12:122500929-122501632	MCF-7	breast:	n/a	chr12:122501211-122501221
12	GATA3	chr12:122500614-122501801	MCF-7	breast:	n/a	n/a
13	HDAC2	chr12:122500642-122502014	MCF-7	breast:	n/a	chr12:122501076-122501085
14	NR3C1	chr12:122500690-122501349	A549	lung:	n/a	n/a
15	MYBL2	chr12:122500893-122501532	HepG2	liver:	n/a	n/a
16	FOSL2	chr12:122500820-122501703	MCF-7	breast:	n/a	chr12:122501405-122501413 chr12:122501406-122501417 chr12:122501403-122501415 chr12:122501405-122501412
17	NR2F2	chr12:122500579-122503676	K562	blood:	n/a	n/a
18	POLR2A	chr12:122500699-122502538	HUVEC	blood vessel:	n/a	n/a
19	REST	chr12:122500595-122501570	A549	lung:	n/a	chr12:122500899-122500912
20	NFIC	chr12:122500867-122501339	HepG2	liver:	n/a	n/a
21	MAFK	chr12:122500902-122501422	HepG2	liver:	n/a	chr12:122501403-122501412
22	GABPA	chr12:122500679-122501683	MCF-7	breast:	n/a	n/a
23	EP300	chr12:122500717-122501670	A549	lung:	n/a	chr12:122501076-122501086
24	MAX	chr12:122500874-122503239	NB4	blood:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174
25	POLR2A	chr12:122500680-122501880	HUVEC	blood vessel:	n/a	n/a
26	MAX	chr12:122500659-122502534	MCF-7	breast:	n/a	chr12:122501211-122501221 chr12:122502164-122502174
27	POLR2A	chr12:122500556-122501673	HUVEC	blood vessel:	n/a	n/a
28	GATA3	chr12:122500665-122502283	MCF-7	breast:	n/a	n/a
29	HDAC2	chr12:122500717-122501553	HepG2	liver:	n/a	chr12:122501076-122501085
30	SIN3AK20	chr12:122500496-122502361	MCF-7	breast:	n/a	n/a
31	POLR2A	chr12:122500884-122501454	HepG2	liver:	n/a	n/a
32	MAX	chr12:122500753-122503262	HCT-116	colon:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174
33	POLR2A	chr12:122500601-122501495	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr12:122500804-122500977	A549	lung:	n/a	n/a
35	HDAC2	chr12:122500646-122501744	MCF-7	breast:	n/a	chr12:122501076-122501085
36	SIN3AK20	chr12:122500590-122501224	SK-N-SH	brain:	n/a	n/a
37	BCL3	chr12:122500508-122502854	A549	lung:	n/a	n/a
38	MAX	chr12:122500593-122503213	HepG2	liver:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174
39	CTCF	chr12:122500909-122502342	A549	lung:	n/a	n/a
40	BCL3	chr12:122500736-122501538	A549	lung:	n/a	n/a
41	E2F6	chr12:122500752-122501495	K562	blood:	n/a	chr12:122501177-122501188
42	POLR2A	chr12:122500701-122501590	MCF-7	breast:	n/a	n/a
43	E2F6	chr12:122500692-122502692	A549	lung:	n/a	chr12:122502213-122502224 chr12:122501177-122501188
44	KAP1	chr12:122500702-122501607	HEK293	kidney:	n/a	chr12:122501403-122501412
45	GABPA	chr12:122500815-122501725	MCF-7	breast:	n/a	n/a
46	POLR2A	chr12:122500304-122503304	HepG2	liver:	n/a	n/a
47	FOSL2	chr12:122500765-122502277	A549	lung:	n/a	chr12:122501405-122501413 chr12:122501406-122501417 chr12:122501403-122501415 chr12:122501405-122501412
48	FOXA1	chr12:122500789-122501310	HepG2	liver:	n/a	n/a
49	KAP1	chr12:122500783-122501575	U2OS	brain:	n/a	chr12:122501403-122501412
50	MAX	chr12:122500579-122503228	A549	lung:	n/a	chr12:122502834-122502843 chr12:122501211-122501221 chr12:122502164-122502174

No.	Distal block	Cell Line	Cell type
1	chr12:122237524..122241320-chr12:122500575..122503777,5	K562	blood:
2	chr12:122500561..122501161-chr12:122582495..122583250,2	MCF-7	breast:
3	chr12:122459539..122463256-chr12:122498402..122502892,4	MCF-7	breast:
4	chr12:122460064..122462817-chr12:122499395..122500991,2	MCF-7	breast:
5	chr12:122459811..122462052-chr12:122500619..122502679,2	K562	blood:
6	chr12:122499616..122503062-chr12:122514965..122517800,5	MCF-7	breast:
7	chr12:122499171..122504349-chr12:122514733..122520643,17	K562	blood:

Variant related genes	Relation type
ENSG00000256546	TF binding region
ENSG00000110987	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs28710224	0.87[AMR][1000 genomes]
rs73417621	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73417628	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73417629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417634	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73417638	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73417656	0.87[AMR][1000 genomes]
rs73417658	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899569	chr12:122478728-122630909	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122472000-122507200	Weak transcription	Fetal Brain Male	brain
2	chr12:122475200-122501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:122491800-122501000	Strong transcription	Fetal Brain Female	brain
4	chr12:122492600-122505600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:122492800-122501000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr12:122492800-122501600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:122497600-122501200	Weak transcription	Fetal Heart	heart
8	chr12:122497600-122502400	Enhancers	Ovary	ovary
9	chr12:122498200-122501000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:122498400-122502400	Weak transcription	HSMMtube	muscle
11	chr12:122498800-122501000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:122498800-122501200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:122499200-122501000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:122499600-122501000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:122499600-122501000	Genic enhancers	Fetal Intestine Small	intestine
16	chr12:122499600-122501200	Enhancers	Colonic Mucosa	Colon
17	chr12:122500000-122501200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:122500000-122501200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:122500000-122501400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:122500000-122501400	Enhancers	Placenta	Placenta
21	chr12:122500000-122501600	Genic enhancers	Thymus	Thymus
22	chr12:122500000-122501800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:122500000-122501800	Enhancers	HMEC	breast
24	chr12:122500000-122502200	Enhancers	Pancreas	Pancrea
25	chr12:122500000-122502600	Enhancers	Liver	Liver
26	chr12:122500000-122502600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr12:122500000-122503400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:122500000-122503600	Enhancers	Right Ventricle	heart
29	chr12:122500000-122504600	Enhancers	Stomach Mucosa	stomach
30	chr12:122500200-122501000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:122500200-122501200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:122500200-122501200	Enhancers	Fetal Stomach	stomach
33	chr12:122500200-122501400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:122500200-122501400	Enhancers	Fetal Intestine Large	intestine
35	chr12:122500200-122501600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:122500200-122501800	Enhancers	NHEK	skin
37	chr12:122500200-122502200	Enhancers	NHDF-Ad	bronchial
38	chr12:122500200-122502600	Enhancers	Gastric	stomach
39	chr12:122500200-122503200	Enhancers	Brain Hippocampus Middle	brain
40	chr12:122500200-122503400	Enhancers	Lung	lung
41	chr12:122500200-122506000	Weak transcription	Dnd41	blood
42	chr12:122500400-122501000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:122500400-122501000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:122500400-122501000	Enhancers	Osteobl	bone
45	chr12:122500400-122501200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:122500400-122501200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:122500400-122501400	Genic enhancers	Fetal Thymus	thymus
48	chr12:122500400-122502200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr12:122500400-122502400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:122500400-122502400	Enhancers	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links