Variant report

Variant	rs7975122
Chromosome Location	chr12:123943214-123943215
allele	C/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	YY1	chr12:123942464-123943220	ECC-1	luminal epithelium:	n/a	chr12:123942854-123942876 chr12:123942972-123942983 chr12:123942857-123942865
2	MAZ	chr12:123942447-123943267	GM12878	blood:	n/a	chr12:123942792-123942801
3	POLR2A	chr12:123942562-123943248	GM10847	blood:	n/a	n/a
4	POLR2A	chr12:123942407-123943799	GM12892	blood:	n/a	n/a
5	YY1	chr12:123942377-123943236	H1-hESC	embryonic stem cell:	n/a	chr12:123942854-123942876 chr12:123942972-123942983 chr12:123942857-123942865
6	POLR2A	chr12:123942581-123943289	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:123942467-123943334	MCF10A-Er-Src	breast:	n/a	n/a
8	TBP	chr12:123942551-123943286	HepG2	liver:	n/a	n/a
9	PML	chr12:123942931-123943305	K562	blood:	n/a	n/a
10	TBP	chr12:123942481-123943267	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:123942418-123943363	HUVEC	blood vessel:	n/a	n/a
12	MXI1	chr12:123942619-123943217	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:123942205-123943581	PFSK-1	brain:	n/a	n/a
14	JUN	chr12:123942323-123943713	K562	blood:	n/a	n/a
15	POLR2A	chr12:123942425-123943229	HL-60	blood:	n/a	n/a
16	POLR2A	chr12:123942390-123943311	PANC-1	pancreas:	n/a	n/a
17	YY1	chr12:123942475-123943244	GM12878	blood:	n/a	chr12:123942854-123942876 chr12:123942972-123942983 chr12:123942857-123942865
18	REST	chr12:123942460-123943216	HL-60	blood:	n/a	chr12:123942830-123942837
19	HEY1	chr12:123942567-123943269	K562	blood:	n/a	n/a
20	POLR2A	chr12:123942540-123943239	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:123942403-123943603	GM12892	blood:	n/a	n/a
22	POLR2A	chr12:123942508-123943310	ECC-1	luminal epithelium:	n/a	n/a
23	NRF1	chr12:123942575-123943330	SK-N-SH	brain:	n/a	chr12:123943070-123943084 chr12:123943073-123943084
24	EGR1	chr12:123942369-123943218	HCT-116	colon:	n/a	chr12:123942598-123942611 chr12:123942599-123942613 chr12:123942600-123942610 chr12:123942598-123942612 chr12:123942972-123942985 chr12:123942599-123942610 chr12:123942600-123942610 chr12:123942599-123942610 chr12:123942641-123942655
25	TAF1	chr12:123942460-123943309	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr12:123942363-123943567	MCF10A-Er-Src	breast:	n/a	n/a
27	HEY1	chr12:123942533-123943695	K562	blood:	n/a	n/a
28	YY1	chr12:123942457-123943225	GM12891	blood:	n/a	chr12:123942854-123942876 chr12:123942972-123942983 chr12:123942857-123942865
29	HNF4A	chr12:123943031-123943238	HepG2	liver:	n/a	n/a
30	SIX5	chr12:123942224-123943555	A549	lung:	n/a	n/a
31	POLR2A	chr12:123942562-123943236	GM12891	blood:	n/a	n/a
32	POLR2A	chr12:123942546-123943626	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:123942514-123943617	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:123942547-123943349	Gliobla	brain:	n/a	n/a
35	POLR2A	chr12:123942356-123943704	K562	blood:	n/a	n/a
36	POLR2A	chr12:123942561-123943605	MCF-7	breast:	n/a	n/a
37	REST	chr12:123942289-123943499	H1-neurons	neurons:	n/a	chr12:123942830-123942837
38	POLR2A	chr12:123942534-123943583	GM19099	blood:	n/a	n/a
39	YY1	chr12:123942423-123943246	SK-N-SH_RA	brain:	n/a	chr12:123942854-123942876 chr12:123942972-123942983 chr12:123942857-123942865
40	TAF1	chr12:123942478-123943316	K562	blood:	n/a	n/a
41	POLR2A	chr12:123942581-123943301	HEK293	kidney:	n/a	n/a
42	POLR2A	chr12:123942385-123943678	PANC-1	pancreas:	n/a	n/a
43	EP300	chr12:123942434-123943215	GM12878	blood:	n/a	chr12:123942689-123942698 chr12:123943106-123943120
44	POLR2A	chr12:123942472-123943242	SK-N-MC	brain:	n/a	n/a
45	TAF1	chr12:123942498-123943318	K562	blood:	n/a	n/a
46	IRF1	chr12:123942450-123943290	K562	blood:	n/a	chr12:123943110-123943122 chr12:123943110-123943121 chr12:123943110-123943122 chr12:123943108-123943122
47	PML	chr12:123942498-123943243	MCF-7	breast:	n/a	n/a
48	POLR2A	chr12:123942549-123943504	PBDE	blood:	n/a	n/a
49	YY1	chr12:123942509-123943301	GM12892	blood:	n/a	chr12:123942854-123942876 chr12:123942972-123942983 chr12:123942857-123942865
50	YY1	chr12:123942502-123943316	GM12878	blood:	n/a	chr12:123942854-123942876 chr12:123942972-123942983 chr12:123942857-123942865

No.	Distal block	Cell Line	Cell type
1	chr12:123941578..123944282-chr12:124067320..124071098,9	MCF-7	breast:
2	chr12:123943032..123944561-chr12:124016969..124018583,2	MCF-7	breast:
3	chr12:123941486..123944276-chr12:124085171..124087519,2	K562	blood:
4	chr12:123919731..123922838-chr12:123939726..123943639,4	MCF-7	breast:
5	chr12:123873193..123874940-chr12:123942406..123944140,2	K562	blood:
6	chr12:123754868..123756621-chr12:123942711..123944463,2	MCF-7	breast:
7	chr12:123849365..123850946-chr12:123941525..123944430,2	K562	blood:
8	chr12:123866599..123869577-chr12:123942434..123944403,3	MCF-7	breast:
9	chr12:123756249..123757789-chr12:123941373..123944326,2	K562	blood:
10	chr12:123919998..123924322-chr12:123941781..123944675,4	K562	blood:
11	chr12:123942949..123945032-chr12:123947880..123951007,3	MCF-7	breast:
12	chr12:123873866..123876385-chr12:123942538..123944226,2	MCF-7	breast:
13	chr12:123868443..123871332-chr12:123941328..123944744,4	K562	blood:
14	chr12:123942564..123944577-chr12:124016063..124019666,4	MCF-7	breast:
15	chr12:123942486..123944135-chr12:124085124..124087552,2	MCF-7	breast:
16	chr12:123941098..123944051-chr12:124068238..124070527,2	K562	blood:
17	chr12:123941485..123944968-chr12:123948238..123952652,6	K562	blood:
18	chr12:123940979..123946241-chr12:123948686..123953480,7	MCF-7	breast:

Variant related genes	Relation type
SNRNP35	TF binding region
ENSG00000150977	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000188026	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000184209	Chromatin interaction
ENSG00000139697	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11507739	0.93[EUR][1000 genomes]
rs11507740	0.99[EUR][1000 genomes]
rs13303080	0.88[EUR][1000 genomes]
rs13303107	0.99[EUR][1000 genomes]
rs13303167	0.92[EUR][1000 genomes]
rs13303200	0.88[EUR][1000 genomes]
rs13303266	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28413969	0.97[EUR][1000 genomes]
rs28483351	0.92[EUR][1000 genomes]
rs28497891	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28557411	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28667043	0.93[EUR][1000 genomes]
rs34047494	0.93[EUR][1000 genomes]
rs34351395	0.88[EUR][1000 genomes]
rs34762274	0.88[EUR][1000 genomes]
rs35090528	0.95[EUR][1000 genomes]
rs35157218	0.92[EUR][1000 genomes]
rs35370271	0.95[EUR][1000 genomes]
rs35970945	0.93[EUR][1000 genomes]
rs36084544	0.87[EUR][1000 genomes]
rs4047517	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56412477	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56860279	0.99[EUR][1000 genomes]
rs6606748	0.96[EUR][1000 genomes]
rs71456799	0.99[EUR][1000 genomes]
rs7297035	0.93[EUR][1000 genomes]
rs7300562	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7306670	0.96[EUR][1000 genomes]
rs7315901	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7960816	0.99[EUR][1000 genomes]
rs7978323	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9330649	0.85[EUR][1000 genomes]
rs9697459	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9697581	0.88[EUR][1000 genomes]
rs9697628	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9697735	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9778001	0.88[EUR][1000 genomes]
rs9803116	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123942200-123943400	Active TSS	Primary monocytes fromperipheralblood	blood
2	chr12:123942200-123943400	Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:123942200-123943400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:123942200-123943400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:123942200-123943400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:123942200-123943400	Active TSS	Brain Germinal Matrix	brain
7	chr12:123942200-123943400	Active TSS	Colonic Mucosa	Colon
8	chr12:123942200-123943400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr12:123942200-123943400	Active TSS	Fetal Muscle Trunk	muscle
10	chr12:123942200-123943400	Active TSS	Fetal Muscle Leg	muscle
11	chr12:123942200-123943400	Active TSS	Fetal Thymus	thymus
12	chr12:123942200-123943400	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr12:123942200-123943600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr12:123942200-123943600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr12:123942200-123943600	Active TSS	Muscle Satellite Cultured Cells	--
16	chr12:123942200-123943600	Active TSS	Fetal Intestine Large	intestine
17	chr12:123942200-123943600	Active TSS	Fetal Intestine Small	intestine
18	chr12:123942200-123943600	Active TSS	Pancreas	Pancrea
19	chr12:123942200-123943600	Active TSS	Thymus	Thymus
20	chr12:123942200-123943800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:123942200-123943800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:123942200-123943800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:123942200-123943800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:123942200-123943800	Active TSS	Fetal Stomach	stomach
25	chr12:123942200-123943800	Active TSS	Psoas Muscle	Psoas
26	chr12:123942200-123943800	Active TSS	Rectal Smooth Muscle	rectum
27	chr12:123942200-123943800	Active TSS	Right Ventricle	heart
28	chr12:123942200-123943800	Active TSS	Stomach Smooth Muscle	stomach
29	chr12:123942200-123943800	Active TSS	A549	lung
30	chr12:123942200-123944000	Active TSS	Duodenum Mucosa	Duodenum
31	chr12:123942200-123944000	Active TSS	Fetal Brain Female	brain
32	chr12:123942200-123944000	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr12:123942200-123944200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:123942200-123944200	Active TSS	Hela-S3	cervix
35	chr12:123942200-123944600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:123942400-123943400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:123942400-123943400	Active TSS	Primary B cells from peripheral blood	blood
38	chr12:123942400-123943400	Active TSS	Primary hematopoietic stem cells	blood
39	chr12:123942400-123943400	Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr12:123942400-123943400	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr12:123942400-123943400	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr12:123942400-123943400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:123942400-123943400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr12:123942400-123943400	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr12:123942400-123943400	Active TSS	Liver	Liver
46	chr12:123942400-123943400	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr12:123942400-123943400	Active TSS	Fetal Brain Male	brain
48	chr12:123942400-123943400	Active TSS	Placenta	Placenta
49	chr12:123942400-123943400	Active TSS	Dnd41	blood
50	chr12:123942400-123943400	Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links