Variant report

Variant	rs188670608
Chromosome Location	chr12:50794494-50794495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:492)
CpG islands
(count:122)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:492 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr12:50794338-50795884	Hela-S3	cervix:	n/a	chr12:50794635-50794651
2	NR2C2	chr12:50794404-50794797	K562	blood:	n/a	chr12:50794592-50794601
3	ZNF143	chr12:50794164-50795128	Hela-S3	cervix:	n/a	n/a
4	EP300	chr12:50794250-50794860	HepG2	liver:	n/a	chr12:50794645-50794661 chr12:50794429-50794436 chr12:50794258-50794272
5	POLR2A	chr12:50794345-50795237	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:50794305-50795185	K562	blood:	n/a	n/a
7	YY1	chr12:50794318-50795028	HepG2	liver:	n/a	n/a
8	TAF1	chr12:50794396-50794821	SK-N-SH	brain:	n/a	n/a
9	MAX	chr12:50794209-50795574	A549	lung:	n/a	chr12:50794883-50794893
10	GABPA	chr12:50793716-50795503	MCF-7	breast:	n/a	n/a
11	HNF4G	chr12:50794329-50794761	HepG2	liver:	n/a	n/a
12	TBP	chr12:50794041-50795199	HepG2	liver:	n/a	n/a
13	ELF1	chr12:50794207-50795177	MCF-7	breast:	n/a	chr12:50794591-50794604 chr12:50794593-50794604 chr12:50794594-50794603
14	NFATC1	chr12:50794082-50794686	GM12878	blood:	n/a	n/a
15	MAX	chr12:50794280-50795262	MCF-7	breast:	n/a	chr12:50794883-50794893
16	POLR2A	chr12:50794256-50795253	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:50794216-50795471	PFSK-1	brain:	n/a	n/a
18	CEBPB	chr12:50794222-50794673	K562	blood:	n/a	n/a
19	MXI1	chr12:50794311-50795706	K562	blood:	n/a	n/a
20	RCOR1	chr12:50794432-50794796	GM12878	blood:	n/a	n/a
21	BRCA1	chr12:50794231-50794785	H1-hESC	embryonic stem cell:	n/a	n/a
22	HMGN3	chr12:50794392-50795281	K562	blood:	n/a	n/a
23	POLR2A	chr12:50794329-50795252	HepG2	liver:	n/a	n/a
24	ELF1	chr12:50794259-50795214	MCF-7	breast:	n/a	chr12:50794591-50794604 chr12:50794593-50794604 chr12:50794594-50794603
25	TAF1	chr12:50794123-50795148	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr12:50794216-50794998	HCT-116	colon:	n/a	n/a
27	CHD2	chr12:50794437-50794930	HepG2	liver:	n/a	n/a
28	MAX	chr12:50794225-50795526	SK-N-SH	brain:	n/a	chr12:50794883-50794893
29	BCL3	chr12:50794155-50795231	A549	lung:	n/a	chr12:50794757-50794766
30	YY1	chr12:50794333-50795304	HepG2	liver:	n/a	n/a
31	YY1	chr12:50794376-50795012	H1-hESC	embryonic stem cell:	n/a	n/a
32	GABPA	chr12:50794273-50795318	K562	blood:	n/a	n/a
33	TAF1	chr12:50794361-50795096	Hela-S3	cervix:	n/a	n/a
34	GTF3C2	chr12:50793568-50794516	Hela-S3	cervix:	n/a	n/a
35	EBF1	chr12:50794362-50794624	GM12878	blood:	n/a	n/a
36	ZNF263	chr12:50794401-50795104	HEK293-T-REx	kidney:	n/a	chr12:50794661-50794670
37	GABPA	chr12:50794378-50794740	Hela-S3	cervix:	n/a	n/a
38	MAX	chr12:50794259-50795379	SK-N-SH	brain:	n/a	chr12:50794883-50794893
39	FOS	chr12:50794416-50794723	MCF10A-Er-Src	breast:	n/a	n/a
40	PML	chr12:50794264-50795048	MCF-7	breast:	n/a	n/a
41	RUNX3	chr12:50794207-50795357	GM12878	blood:	n/a	n/a
42	MAX	chr12:50794291-50795820	Hela-S3	cervix:	n/a	chr12:50794883-50794893
43	TAF1	chr12:50794362-50795013	MCF-7	breast:	n/a	n/a
44	BHLHE40	chr12:50794102-50794939	HepG2	liver:	n/a	chr12:50794635-50794651
45	POLR2A	chr12:50794022-50795408	Raji	blood:	n/a	n/a
46	POLR2A	chr12:50794291-50795530	HepG2	liver:	n/a	n/a
47	POLR2A	chr12:50794245-50795243	HUVEC	blood vessel:	n/a	n/a
48	MAX	chr12:50794237-50795579	HepG2	liver:	n/a	chr12:50794883-50794893
49	POLR2A	chr12:50794273-50795166	GM12878	blood:	n/a	n/a
50	BRCA1	chr12:50794476-50794717	HepG2	liver:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:50794485-50794535	H1-hESC	embryonic stem cell:	embryo
2	chr12:50794494-50794544	HNPCEpiC	eye:	n/a
3	chr12:50794485-50794535	MCF10A-Er-Src	breast:	n/a
4	chr12:50794494-50794544	HRPEpiC	eye:	n/a
5	chr12:50794485-50794535	HCF	heart:	n/a
6	chr12:50794485-50794535	MCF-7	breast:	n/a
7	chr12:50794485-50794535	HEK293	kidney:	embryo
8	chr12:50794494-50794544	AG09309	skin:	n/a
9	chr12:50794485-50794535	CMK	blood:	n/a
10	chr12:50794485-50794535	SK-N-SH_RA	brain:	n/a
11	chr12:50794494-50794544	AG04450	lung:	fetal
12	chr12:50794485-50794535	HUVEC	blood vessel:	n/a
13	chr12:50794494-50794544	Hela-S3	cervix:	n/a
14	chr12:50794494-50794544	HCF	heart:	n/a
15	chr12:50794485-50794535	U87	brain:	n/a
16	chr12:50794494-50794544	H1-hESC	embryonic stem cell:	embryo
17	chr12:50794485-50794535	NB4	blood:	n/a
18	chr12:50794494-50794544	GM12891	blood:	n/a
19	chr12:50794485-50794535	GM12878	blood:	n/a
20	chr12:50794494-50794544	SKMC	muscle:	n/a
21	chr12:50794485-50794535	PFSK-1	brain:	n/a
22	chr12:50794485-50794535	GM12892	blood:	n/a
23	chr12:50794485-50794535	HCPEpiC	choroid plexus:	n/a
24	chr12:50794494-50794544	HRCEpiC	kidney:	n/a
25	chr12:50794494-50794544	SAEC	small airway:	n/a
26	chr12:50794485-50794535	AG10803	skin:	n/a
27	chr12:50794485-50794535	GM19239	blood:	n/a
28	chr12:50794494-50794544	ECC-1	luminal epithelium:	n/a
29	chr12:50794494-50794544	GM19239	blood:	n/a
30	chr12:50794494-50794544	HAEpiC	amniotic membrane:	n/a
31	chr12:50794485-50794535	AG04450	lung:	fetal
32	chr12:50794494-50794544	HPAEpiC	pulmonary alveolar:	n/a
33	chr12:50794485-50794535	SAEC	small airway:	n/a
34	chr12:50794485-50794535	GM06990	blood:	n/a
35	chr12:50794494-50794544	AG10803	skin:	n/a
36	chr12:50794494-50794544	SK-N-MC	brain:	n/a
37	chr12:50794485-50794535	SK-N-MC	brain:	n/a
38	chr12:50794485-50794535	IMR90	lung:	fetal
39	chr12:50794494-50794544	BE2_C	brain:	n/a
40	chr12:50794494-50794544	AG09319	gingival:	n/a
41	chr12:50794485-50794535	SKMC	muscle:	n/a
42	chr12:50794494-50794544	SK-N-SH	brain:	n/a
43	chr12:50794485-50794535	HNPCEpiC	eye:	n/a
44	chr12:50794485-50794535	NT2-D1	testis:	n/a
45	chr12:50794494-50794544	HepG2	liver:	n/a
46	chr12:50794494-50794544	HMEC	breast:	n/a
47	chr12:50794494-50794544	HCM	heart:	n/a
48	chr12:50794494-50794544	HRE	kidney:	n/a
49	chr12:50794485-50794535	LNCaP	prostate:	n/a
50	chr12:50794494-50794544	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr12:50416797..50419367-chr12:50793748..50795984,3	K562	blood:
2	chr12:50677350..50679861-chr12:50792501..50795030,2	K562	blood:
3	chr12:50495184..50497904-chr12:50792002..50794811,2	K562	blood:
4	chr12:50560048..50562244-chr12:50793488..50796318,2	MCF-7	breast:
5	chr1:27188967..27189716-chr12:50794394..50795151,2	Hela-S3	cervix:
6	chr12:50793053..50795901-chr12:51566225..51568182,2	K562	blood:
7	chr12:50504921..50507290-chr12:50793420..50795913,2	K562	blood:
8	chr12:50614841..50617436-chr12:50793138..50795396,3	K562	blood:
9	chr12:50793597..50795392-chr12:51156771..51159161,2	MCF-7	breast:
10	chr12:50611453..50613308-chr12:50792675..50795177,2	K562	blood:
11	chr10:90639968..90640523-chr12:50794439..50795346,2	Hela-S3	cervix:
12	chr12:50639732..50644182-chr12:50792343..50795361,4	K562	blood:
13	chr12:50561032..50562687-chr12:50794487..50796124,2	K562	blood:
14	chr12:50614841..50617436-chr12:50793138..50796219,5	K562	blood:
15	chr12:50787607..50792856-chr12:50793045..50797935,10	K562	blood:
16	chr12:50794445..50795114-chr15:64673256..64673791,2	NB4	blood:
17	chr12:50758172..50761780-chr12:50791230..50796188,4	K562	blood:
18	chr11:62609053..62609617-chr12:50794323..50794873,2	Hela-S3	cervix:
19	chr12:50744030..50745748-chr12:50793472..50795953,2	K562	blood:
20	chr12:50504921..50507362-chr12:50794413..50796105,2	K562	blood:
21	chr12:50794419..50795025-chr4:151936304..151937173,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
FAM186A	TF binding region
LARP4	TF binding region
FAM186A	CpG island
LARP4	CpG island
ENSG00000123268	Chromatin interaction
ENSG00000244266	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000175793	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000198589	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000178449	Chromatin interaction
ENSG00000185958	Chromatin interaction
ENSG00000166803	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000138134	Chromatin interaction
ENSG00000161800	Chromatin interaction
ENSG00000135457	Chromatin interaction
ENSG00000257531	Chromatin interaction
ENSG00000203433	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
11	esv3445416	chr12:50794231-50794786	Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50793600-50796800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:50793800-50794800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:50793800-50794800	Active TSS	HepG2	liver
4	chr12:50793800-50795000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:50793800-50795400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:50793800-50795400	Active TSS	Duodenum Mucosa	Duodenum
7	chr12:50793800-50795400	Active TSS	Fetal Brain Female	brain
8	chr12:50793800-50796200	Active TSS	Brain Germinal Matrix	brain
9	chr12:50793800-50796200	Active TSS	NHEK	skin
10	chr12:50793800-50796400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:50793800-50796400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:50793800-50796400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr12:50793800-50796600	Active TSS	Hela-S3	cervix
14	chr12:50793800-50797000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr12:50793800-50797000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:50793800-50797000	Active TSS	Fetal Intestine Large	intestine
17	chr12:50793800-50797400	Active TSS	K562	blood
18	chr12:50793800-50798000	Active TSS	GM12878-XiMat	blood
19	chr12:50794000-50794600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:50794000-50794600	Active TSS	Right Atrium	heart
21	chr12:50794000-50795200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:50794000-50795200	Active TSS	Adipose Nuclei	Adipose
23	chr12:50794000-50795400	Active TSS	Brain Hippocampus Middle	brain
24	chr12:50794000-50795400	Active TSS	Thymus	Thymus
25	chr12:50794000-50795400	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr12:50794000-50795600	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr12:50794000-50795800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:50794000-50795800	Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr12:50794000-50796000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr12:50794000-50796000	Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr12:50794000-50796000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr12:50794000-50796000	Active TSS	Fetal Brain Male	brain
33	chr12:50794000-50796000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr12:50794000-50796000	Active TSS	Fetal Muscle Trunk	muscle
35	chr12:50794000-50796200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:50794000-50796200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr12:50794000-50796200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr12:50794000-50796200	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr12:50794000-50796200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr12:50794000-50796200	Active TSS	Fetal Stomach	stomach
41	chr12:50794000-50796200	Active TSS	Rectal Smooth Muscle	rectum
42	chr12:50794000-50796200	Active TSS	Stomach Smooth Muscle	stomach
43	chr12:50794000-50796400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr12:50794000-50796400	Active TSS	Brain Angular Gyrus	brain
45	chr12:50794000-50796400	Active TSS	Brain Cingulate Gyrus	brain
46	chr12:50794000-50796400	Active TSS	Fetal Muscle Leg	muscle
47	chr12:50794000-50796400	Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr12:50794000-50796400	Active TSS	Stomach Mucosa	stomach
49	chr12:50794000-50796400	Active TSS	NH-A	brain
50	chr12:50794000-50796600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links