Variant report

Variant	rs12306316
Chromosome Location	chr12:29301842-29301843
allele	A/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	CTCF	chr12:29301840-29301990	HAc	cerebellar:	n/a	n/a
2	RUNX3	chr12:29301662-29302196	GM12878	blood:	n/a	n/a
3	CTCF	chr12:29301780-29301930	GM12868	blood:	n/a	n/a
4	CTCF	chr12:29301780-29301930	AG09319	gingival:	n/a	n/a
5	TAF1	chr12:29301274-29303258	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:29301084-29302716	HUVEC	blood vessel:	n/a	n/a
7	RAD21	chr12:29301655-29301878	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr12:29301057-29303694	NB4	blood:	n/a	n/a
9	POLR2A	chr12:29301714-29302407	H1-neurons	neurons:	n/a	n/a
10	MYC	chr12:29301019-29303692	NB4	blood:	n/a	chr12:29302778-29302787
11	POLR2A	chr12:29301680-29302428	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr12:29301319-29303437	H1-hESC	embryonic stem cell:	n/a	n/a
13	HEY1	chr12:29301821-29302766	K562	blood:	n/a	chr12:29302131-29302146
14	RELA	chr12:29301580-29302627	GM19099	blood:	n/a	n/a
15	MAX	chr12:29301000-29303723	NB4	blood:	n/a	chr12:29302778-29302787
16	CTCF	chr12:29301740-29301890	AG09319	gingival:	n/a	n/a
17	CTCF	chr12:29301740-29301890	GM12874	blood:	n/a	n/a
18	POLR2A	chr12:29301785-29302848	K562	blood:	n/a	n/a
19	CTCF	chr12:29301780-29301930	BJ	skin:	n/a	n/a
20	CTCF	chr12:29301673-29301889	GM19238	blood:	n/a	n/a
21	POLR2A	chr12:29301746-29302708	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr12:29301120-29303297	GM18951	blood:	n/a	n/a
23	POLR2A	chr12:29301473-29303046	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr12:29301820-29301970	RPTEC	kidney:	n/a	n/a
25	POLR2A	chr12:29301337-29303433	HL-60	blood:	n/a	n/a
26	CTCF	chr12:29301740-29301890	GM12866	blood:	n/a	n/a
27	RUNX3	chr12:29301743-29302104	GM12878	blood:	n/a	n/a
28	EGR1	chr12:29301809-29302165	K562	blood:	n/a	chr12:29302042-29302055 chr12:29302042-29302052 chr12:29302043-29302052
29	YY1	chr12:29301784-29302100	SK-N-SH_RA	brain:	n/a	chr12:29301928-29301939
30	CTCF	chr12:29301740-29301890	HRPEpiC	eye:	n/a	n/a
31	TBP	chr12:29301278-29303167	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr12:29301757-29302662	K562	blood:	n/a	n/a
33	POLR2A	chr12:29301840-29302410	MCF10A-Er-Src	breast:	n/a	n/a
34	TAF7	chr12:29301789-29302570	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr12:29301760-29301910	GM12872	blood:	n/a	n/a
36	POLR2A	chr12:29300990-29303986	H1-hESC	embryonic stem cell:	n/a	n/a
37	HEY1	chr12:29301823-29302575	K562	blood:	n/a	chr12:29302131-29302146
38	POLR2A	chr12:29301410-29303310	GM18526	blood:	n/a	n/a
39	CTCF	chr12:29301740-29301890	GM06990	blood:	n/a	n/a
40	POLR2A	chr12:29301797-29302338	U87	brain:	n/a	n/a
41	RAD21	chr12:29301434-29302235	SK-N-SH_RA	brain:	n/a	n/a
42	POLR2A	chr12:29301007-29302822	HUVEC	blood vessel:	n/a	n/a
43	CTCF	chr12:29301708-29301849	GM19240	blood:	n/a	n/a
44	CTCF	chr12:29301720-29301870	NB4	blood:	n/a	n/a
45	CHD1	chr12:29301105-29301850	H1-hESC	embryonic stem cell:	n/a	chr12:29301793-29301800
46	POLR2A	chr12:29301406-29303379	GM19193	blood:	n/a	n/a
47	CTCF	chr12:29301760-29301910	HPAF	blood vessel:	n/a	n/a
48	CTCF	chr12:29301700-29301850	HRE	kidney:	n/a	n/a
49	MAX	chr12:29301785-29303294	H1-hESC	embryonic stem cell:	n/a	chr12:29302778-29302787
50	REST	chr12:29301696-29303250	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
FAR2	TF binding region
ENSG00000257258	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10843330	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10843331	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10843332	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10843333	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10843334	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10843336	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10843338	0.82[EUR][1000 genomes]
rs11050035	0.86[EUR][1000 genomes]
rs11050039	0.86[EUR][1000 genomes]
rs11050040	0.86[EUR][1000 genomes]
rs11050046	0.88[EUR][1000 genomes]
rs11050076	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050077	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050078	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050095	0.82[EUR][1000 genomes]
rs11050096	0.82[EUR][1000 genomes]
rs11050103	0.82[EUR][1000 genomes]
rs12049941	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12228075	0.86[EUR][1000 genomes]
rs1390536	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1390537	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1587186	0.88[EUR][1000 genomes]
rs34844277	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73071989	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309466	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
4	nsv819469	chr12:29285461-29303486	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3337951	chr12:29288734-29303032	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv33168	chr12:29301452-29303155	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29300600-29303200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:29301000-29302000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr12:29301000-29302600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:29301000-29302600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:29301000-29303000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:29301000-29303000	Active TSS	Brain Substantia Nigra	brain
7	chr12:29301000-29303200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr12:29301000-29303200	Active TSS	Psoas Muscle	Psoas
9	chr12:29301000-29303400	Active TSS	Fetal Kidney	kidney
10	chr12:29301000-29303400	Active TSS	Stomach Smooth Muscle	stomach
11	chr12:29301000-29303600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:29301000-29304200	Active TSS	Brain Cingulate Gyrus	brain
13	chr12:29301200-29302000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:29301200-29302000	Active TSS	Brain Germinal Matrix	brain
15	chr12:29301200-29302400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:29301200-29302400	Bivalent/Poised TSS	Fetal Lung	lung
17	chr12:29301200-29302800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr12:29301200-29303000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:29301200-29303000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:29301200-29303000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr12:29301200-29303200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:29301200-29303200	Active TSS	Right Atrium	heart
23	chr12:29301200-29303200	Active TSS	K562	blood
24	chr12:29301200-29303400	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr12:29301200-29303400	Active TSS	Colonic Mucosa	Colon
26	chr12:29301200-29303400	Active TSS	Colon Smooth Muscle	Colon
27	chr12:29301200-29303400	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:29301200-29303400	Active TSS	Right Ventricle	heart
29	chr12:29301200-29303600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:29301400-29302000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:29301400-29302600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:29301400-29302600	Active TSS	Fetal Brain Female	brain
33	chr12:29301400-29302600	Active TSS	HSMMtube	muscle
34	chr12:29301400-29302800	Active TSS	Aorta	Aorta
35	chr12:29301400-29302800	Active TSS	Gastric	stomach
36	chr12:29301400-29302800	Active TSS	Lung	lung
37	chr12:29301400-29303000	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr12:29301400-29303000	Active TSS	Duodenum Mucosa	Duodenum
39	chr12:29301400-29303000	Active TSS	Esophagus	oesophagus
40	chr12:29301400-29303000	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr12:29301400-29303000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
42	chr12:29301400-29303000	Active TSS	Spleen	Spleen
43	chr12:29301400-29303200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:29301400-29303200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr12:29301400-29303200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:29301400-29303200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:29301400-29303200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:29301400-29303200	Active TSS	Small Intestine	intestine
49	chr12:29301400-29303200	Active TSS	NHDF-Ad	bronchial
50	chr12:29301400-29303800	Active TSS	Brain Anterior Caudate	brain

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