Variant report

Variant	rs2576943
Chromosome Location	chr12:104371163-104371164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104371062-104371382	K562	blood:	n/a	n/a
2	POLR2A	chr12:104371018-104371410	K562	blood:	n/a	n/a
3	POLR2A	chr12:104371076-104371388	K562	blood:	n/a	n/a
4	POLR2A	chr12:104370974-104371799	GM12891	blood:	n/a	n/a
5	POLR2A	chr12:104371123-104371377	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:104370907-104371414	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:104371117-104372395	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:104371139-104371339	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:104371107-104371266	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:104371008-104371549	K562	blood:	n/a	n/a
11	POLR2A	chr12:104370967-104371925	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:104371061-104371325	GM12891	blood:	n/a	n/a
13	POLR2A	chr12:104371022-104371419	K562	blood:	n/a	n/a
14	POLR2A	chr12:104370997-104372789	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:104371137-104371326	HepG2	liver:	n/a	n/a
16	POLR2A	chr12:104371045-104371358	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:104370657-104372861	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:104371012-104371552	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr12:104370975-104372773	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:104371124-104371830	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:104371093-104371704	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104348589..104351037-chr12:104369776..104372245,2	MCF-7	breast:
2	chr12:104370024..104373447-chr12:104374664..104377599,4	K562	blood:
3	chr12:104362237..104366185-chr12:104369419..104371303,3	MCF-7	breast:

No data

Variant related genes	Relation type
TDG	TF binding region
ENSG00000204954	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11111861	1.00[ASN][1000 genomes]
rs1125322	1.00[ASN][1000 genomes]
rs11611650	1.00[ASN][1000 genomes]
rs1165672	1.00[ASN][1000 genomes]
rs12825687	1.00[ASN][1000 genomes]
rs1385663	1.00[ASN][1000 genomes]
rs167715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882018	1.00[ASN][1000 genomes]
rs2204802	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2243680	1.00[ASN][1000 genomes]
rs2248995	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251215	1.00[ASN][1000 genomes]
rs2252213	1.00[ASN][1000 genomes]
rs2374327	1.00[ASN][1000 genomes]
rs2439621	1.00[ASN][1000 genomes]
rs2583224	1.00[ASN][1000 genomes]
rs2583225	1.00[ASN][1000 genomes]
rs2583233	1.00[ASN][1000 genomes]
rs2583234	1.00[ASN][1000 genomes]
rs2583237	1.00[ASN][1000 genomes]
rs2583244	1.00[ASN][1000 genomes]
rs2583258	1.00[ASN][1000 genomes]
rs2583274	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583278	1.00[ASN][1000 genomes]
rs2629750	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700494	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700507	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700517	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722177	1.00[ASN][1000 genomes]
rs2722180	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722194	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723849	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723850	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2723853	1.00[ASN][1000 genomes]
rs2723877	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs322104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35140616	1.00[ASN][1000 genomes]
rs4135039	1.00[ASN][1000 genomes]
rs4135040	1.00[ASN][1000 genomes]
rs4135047	1.00[ASN][1000 genomes]
rs4135048	1.00[ASN][1000 genomes]
rs4135050	1.00[ASN][1000 genomes]
rs4135061	1.00[ASN][1000 genomes]
rs4135062	1.00[ASN][1000 genomes]
rs4135066	1.00[ASN][1000 genomes]
rs784080	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs784084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931306	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv3336985	chr12:104370741-104373782	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104360800-104371200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:104360800-104371200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:104360800-104371200	Weak transcription	Colonic Mucosa	Colon
4	chr12:104360800-104371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:104360800-104378600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:104360800-104381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:104361000-104372000	Weak transcription	Stomach Mucosa	stomach
8	chr12:104361200-104379400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:104361600-104385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:104361800-104371200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:104362000-104373800	Weak transcription	Psoas Muscle	Psoas
12	chr12:104362000-104382600	Weak transcription	Esophagus	oesophagus
13	chr12:104362000-104384400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
15	chr12:104362200-104371200	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:104362200-104384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:104362400-104371200	Weak transcription	Brain Germinal Matrix	brain
18	chr12:104362400-104371400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:104362400-104378000	Weak transcription	Small Intestine	intestine
20	chr12:104363400-104371200	Weak transcription	Brain Substantia Nigra	brain
21	chr12:104363400-104371200	Weak transcription	Fetal Brain Female	brain
22	chr12:104363400-104371400	Weak transcription	Spleen	Spleen
23	chr12:104363600-104371200	Weak transcription	Aorta	Aorta
24	chr12:104363600-104371200	Weak transcription	Brain Angular Gyrus	brain
25	chr12:104363800-104371400	Weak transcription	HMEC	breast
26	chr12:104363800-104382400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:104364000-104371200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:104364000-104372800	Strong transcription	Fetal Intestine Small	intestine
29	chr12:104364000-104381000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:104364600-104383800	Strong transcription	Dnd41	blood
31	chr12:104365800-104371200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:104366200-104376000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:104366600-104383600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:104366800-104380400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:104366800-104381600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:104367000-104377000	Strong transcription	Fetal Stomach	stomach
37	chr12:104367600-104381000	Strong transcription	GM12878-XiMat	blood
38	chr12:104368200-104373800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr12:104368200-104380600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:104368400-104371200	Weak transcription	Ovary	ovary
41	chr12:104368400-104373800	Weak transcription	NHEK	skin
42	chr12:104368800-104381000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr12:104368800-104381600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:104369200-104372200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:104369200-104381000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:104369200-104381000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr12:104369200-104381000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr12:104369200-104383800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:104369400-104376400	Weak transcription	Fetal Heart	heart
50	chr12:104369400-104380800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links