Variant report

Variant	rs12053442
Chromosome Location	chr2:173295405-173295406
allele	C/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	CEBPB	chr2:173295167-173295994	HCT-116	colon:	n/a	n/a
2	FOS	chr2:173295379-173295844	MCF10A-Er-Src	breast:	n/a	chr2:173295653-173295664 chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295599-173295606 chr2:173295598-173295606
3	TCF12	chr2:173295333-173295940	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr2:173295338-173295731	MCF10A-Er-Src	breast:	n/a	n/a
5	FOSL1	chr2:173295248-173296070	HCT-116	colon:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295599-173295606 chr2:173295598-173295606
6	FOSL2	chr2:173295393-173295837	HepG2	liver:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295599-173295606 chr2:173295598-173295606
7	JUND	chr2:173295381-173295814	Hela-S3	cervix:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295653-173295664 chr2:173295599-173295606 chr2:173295598-173295606
8	FOSL1	chr2:173295302-173295912	HCT-116	colon:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295599-173295606 chr2:173295598-173295606
9	CEBPB	chr2:173295233-173295954	HCT-116	colon:	n/a	n/a
10	SP1	chr2:173295355-173295970	HCT-116	colon:	n/a	n/a
11	GATA3	chr2:173295331-173296067	SK-N-SH	brain:	n/a	chr2:173295599-173295608
12	POLR2A	chr2:173295345-173295718	MCF10A-Er-Src	breast:	n/a	n/a
13	JUND	chr2:173295285-173296079	HCT-116	colon:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295653-173295664 chr2:173295599-173295606 chr2:173295598-173295606
14	JUND	chr2:173295391-173295944	SK-N-SH	brain:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295653-173295664 chr2:173295599-173295606 chr2:173295598-173295606
15	JUND	chr2:173295249-173295963	HCT-116	colon:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295653-173295664 chr2:173295599-173295606 chr2:173295598-173295606
16	STAT3	chr2:173295029-173295900	MCF10A-Er-Src	breast:	n/a	chr2:173295655-173295664 chr2:173295506-173295514 chr2:173295676-173295684 chr2:173295674-173295685
17	FOSL2	chr2:173295338-173295964	SK-N-SH	brain:	n/a	chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295599-173295606 chr2:173295598-173295606
18	NFIC	chr2:173295326-173296087	SK-N-SH	brain:	n/a	chr2:173295761-173295777 chr2:173295760-173295777
19	SP1	chr2:173295222-173295950	HCT-116	colon:	n/a	n/a
20	POLR2A	chr2:173295394-173295883	HCT-116	colon:	n/a	n/a
21	GATA3	chr2:173295343-173296107	SK-N-SH	brain:	n/a	chr2:173295599-173295608
22	FOS	chr2:173295373-173295886	MCF10A-Er-Src	breast:	n/a	chr2:173295653-173295664 chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295599-173295606 chr2:173295598-173295606
23	FOS	chr2:173295394-173295886	MCF10A-Er-Src	breast:	n/a	chr2:173295653-173295664 chr2:173295779-173295788 chr2:173295594-173295605 chr2:173295599-173295606 chr2:173295598-173295606

No.	Distal block	Cell Line	Cell type
1	chr2:173218614..173220137-chr2:173294190..173296145,2	K562	blood:
2	chr2:173291261..173294444-chr2:173294873..173298615,3	K562	blood:
3	chr2:173272055..173273820-chr2:173294658..173297401,2	MCF-7	breast:
4	chr2:173294248..173297165-chr2:173302746..173304421,2	MCF-7	breast:
5	chr2:173290254..173291940-chr2:173293674..173296240,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226963	TF binding region
ENSG00000226963	Chromatin interaction
ENSG00000091409	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	0.85[EUR][1000 genomes]
rs10207640	0.85[EUR][1000 genomes]
rs10207654	0.85[EUR][1000 genomes]
rs12052253	0.85[EUR][1000 genomes]
rs12052385	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12613307	0.82[EUR][1000 genomes]
rs12615584	1.00[AFR][1000 genomes]
rs12615596	0.82[EUR][1000 genomes]
rs12621278	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12622724	0.82[EUR][1000 genomes]
rs13410475	0.85[EUR][1000 genomes]
rs13414928	0.82[EUR][1000 genomes]
rs1574256	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1574259	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860397	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860419	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860426	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16860438	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16860478	1.00[AFR][1000 genomes]
rs16860515	1.00[AFR][1000 genomes]
rs16860634	1.00[AFR][1000 genomes]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293647	1.00[AFR][1000 genomes]
rs2293648	1.00[AFR][1000 genomes]
rs3108779	0.93[ASN][1000 genomes]
rs3762618	0.85[EUR][1000 genomes]
rs4405725	0.82[EUR][1000 genomes]
rs55867175	1.00[AFR][1000 genomes]
rs56882727	1.00[AFR][1000 genomes]
rs57244773	1.00[AFR][1000 genomes]
rs57404607	1.00[AFR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes]
rs59374567	1.00[AFR][1000 genomes]
rs59454075	0.85[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes]
rs6721624	0.97[ASN][1000 genomes]
rs9636257	1.00[AFR][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv875414	chr2:173267081-173307756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv1847874	chr2:173277361-173308318	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583663	chr2:173287832-173307756	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583664	chr2:173289239-173307756	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173292000-173295600	Active TSS	Fetal Intestine Large	intestine
2	chr2:173292000-173296600	Active TSS	Right Atrium	heart
3	chr2:173292200-173295600	Active TSS	Lung	lung
4	chr2:173292200-173295800	Active TSS	HMEC	breast
5	chr2:173292200-173296000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:173292200-173296000	Active TSS	Duodenum Mucosa	Duodenum
7	chr2:173292200-173296200	Active TSS	Right Ventricle	heart
8	chr2:173293200-173295600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:173293200-173295800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr2:173293400-173297800	Transcr. at gene 5' and 3'	NHEK	skin
11	chr2:173293600-173295600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr2:173293600-173296000	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr2:173293800-173295600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr2:173294000-173296000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
15	chr2:173294000-173297600	Weak transcription	Spleen	Spleen
16	chr2:173294000-173301800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:173294200-173295600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr2:173294200-173302600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:173294400-173295800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:173294400-173295800	Active TSS	HSMMtube	muscle
21	chr2:173294400-173296400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr2:173294400-173296600	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr2:173294400-173298000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:173294400-173299200	Weak transcription	Placenta	Placenta
25	chr2:173294400-173301400	Weak transcription	Aorta	Aorta
26	chr2:173294600-173296000	Enhancers	A549	lung
27	chr2:173294600-173296400	Active TSS	Adipose Nuclei	Adipose
28	chr2:173294600-173297200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:173294600-173297200	Weak transcription	Gastric	stomach
30	chr2:173294600-173298000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:173294600-173302400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:173294600-173302600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:173294600-173302600	Weak transcription	NH-A	brain
34	chr2:173294600-173303000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:173294600-173303400	Weak transcription	NHLF	lung
36	chr2:173294800-173295600	Active TSS	Left Ventricle	heart
37	chr2:173294800-173295600	Active TSS	Psoas Muscle	Psoas
38	chr2:173294800-173295800	Weak transcription	Liver	Liver
39	chr2:173294800-173295800	Weak transcription	Pancreas	Pancrea
40	chr2:173294800-173296000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:173294800-173296000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:173294800-173296200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:173294800-173296200	Weak transcription	Fetal Thymus	thymus
44	chr2:173294800-173296400	Enhancers	Hela-S3	cervix
45	chr2:173294800-173296800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:173294800-173296800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:173294800-173296800	Weak transcription	Brain Substantia Nigra	brain
48	chr2:173294800-173297400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:173294800-173297400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr2:173294800-173297400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links