Variant report

Variant	rs11174558
Chromosome Location	chr12:62993942-62993943
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	chr12:62993880-62994030	AG04449	skin:	n/a	chr12:62993981-62993988
2	CTCF	chr12:62993900-62994050	HUVEC	blood vessel:	n/a	chr12:62993981-62993988
3	CTCF	chr12:62993840-62993990	HCM	heart:	n/a	chr12:62993981-62993988
4	CTCF	chr12:62993940-62994090	HFF-Myc	foreskin:	n/a	chr12:62993981-62993988
5	CTCF	chr12:62993940-62994090	AG04449	skin:	n/a	chr12:62993981-62993988
6	CTCF	chr12:62993860-62994010	NB4	blood:	n/a	chr12:62993981-62993988
7	CTCF	chr12:62993880-62994030	GM12873	blood:	n/a	chr12:62993981-62993988
8	CTCF	chr12:62993920-62994070	HAc	cerebellar:	n/a	chr12:62993981-62993988
9	CTCF	chr12:62993820-62993970	GM12878	blood:	n/a	n/a
10	CTCF	chr12:62993880-62994030	HMEC	breast:	n/a	chr12:62993981-62993988
11	CTCF	chr12:62993900-62994050	GM12872	blood:	n/a	chr12:62993981-62993988
12	CTCF	chr12:62993920-62994070	GM12878	blood:	n/a	chr12:62993981-62993988
13	CTCF	chr12:62993920-62994070	MCF-7	breast:	n/a	chr12:62993981-62993988
14	CTCF	chr12:62993880-62994030	MCF-7	breast:	n/a	chr12:62993981-62993988
15	CTCF	chr12:62993820-62993970	GM12868	blood:	n/a	n/a
16	CTCF	chr12:62993860-62994010	GM06990	blood:	n/a	chr12:62993981-62993988
17	CTCF	chr12:62993860-62994010	HPF	lung:	n/a	chr12:62993981-62993988
18	RAD21	chr12:62993748-62994231	H1-hESC	embryonic stem cell:	n/a	chr12:62993979-62993988
19	CTCF	chr12:62993900-62994050	HEK293	kidney:	n/a	chr12:62993981-62993988
20	CTCF	chr12:62993867-62994106	MCF-7	breast:	n/a	chr12:62993981-62993988
21	CTCF	chr12:62993840-62993990	GM12867	blood:	n/a	chr12:62993981-62993988
22	CTCF	chr12:62993880-62994030	A549	lung:	n/a	chr12:62993981-62993988
23	CTCF	chr12:62993940-62994090	HCPEpiC	choroid plexus:	n/a	chr12:62993981-62993988
24	CTCF	chr12:62993940-62994090	HMF	breast:	n/a	chr12:62993981-62993988
25	CTCF	chr12:62993878-62994141	H1-hESC	embryonic stem cell:	n/a	chr12:62993981-62993988
26	CTCF	chr12:62993900-62994050	NHLF	lung:	n/a	chr12:62993981-62993988
27	CTCF	chr12:62993920-62994070	NHDF-neo	bronchial:	n/a	chr12:62993981-62993988
28	CTCF	chr12:62993920-62994070	Hela-S3	cervix:	n/a	chr12:62993981-62993988
29	CTCF	chr12:62993860-62994010	AoAF	blood vessel:	n/a	chr12:62993981-62993988
30	RAD21	chr12:62993772-62994139	H1-hESC	embryonic stem cell:	n/a	chr12:62993979-62993988
31	CTCF	chr12:62993860-62994010	HMEC	breast:	n/a	chr12:62993981-62993988
32	CTCF	chr12:62993880-62994030	HPAF	blood vessel:	n/a	chr12:62993981-62993988
33	CTCF	chr12:62993900-62994050	HCT-116	colon:	n/a	chr12:62993981-62993988
34	CTCF	chr12:62993920-62994070	HFF	foreskin:	n/a	chr12:62993981-62993988
35	CTCF	chr12:62993920-62994070	HMF	breast:	n/a	chr12:62993981-62993988
36	RAD21	chr12:62993836-62994081	SK-N-SH_RA	brain:	n/a	chr12:62993979-62993988
37	CTCF	chr12:62993840-62993990	AG04450	lung:	n/a	chr12:62993981-62993988
38	CTCF	chr12:62993880-62994030	AG10803	skin:	n/a	chr12:62993981-62993988
39	CTCF	chr12:62993880-62994030	HepG2	liver:	n/a	chr12:62993981-62993988
40	CTCF	chr12:62993860-62994010	Caco-2	colon:	n/a	chr12:62993981-62993988
41	CTCF	chr12:62993885-62994005	HepG2	liver:	n/a	chr12:62993981-62993988
42	CTCF	chr12:62993900-62994050	K562	blood:	n/a	chr12:62993981-62993988
43	CTCF	chr12:62993900-62994050	AoAF	blood vessel:	n/a	chr12:62993981-62993988
44	CTCF	chr12:62993920-62994070	AG09309	skin:	n/a	chr12:62993981-62993988
45	CTCF	chr12:62993940-62994090	AG04450	lung:	n/a	chr12:62993981-62993988
46	CTCF	chr12:62993940-62994090	AG09319	gingival:	n/a	chr12:62993981-62993988
47	CTCF	chr12:62993920-62994070	A549	lung:	n/a	chr12:62993981-62993988
48	CTCF	chr12:62993840-62993990	BE2_C	brain:	n/a	chr12:62993981-62993988
49	CTCF	chr12:62993812-62994198	MCF-7	breast:	n/a	chr12:62993981-62993988
50	CTCF	chr12:62993900-62994050	HA-sp	spinal cord:	n/a	chr12:62993981-62993988

No.	Distal block	Cell Line	Cell type
1	chr12:62975484..62979404-chr12:62993353..62996237,5	K562	blood:
2	chr12:62992552..62995339-chr12:63185731..63187957,2	MCF-7	breast:
3	chr12:62989825..62992021-chr12:62992678..62994199,2	MCF-7	breast:
4	chr12:62991974..62994921-chr5:128794290..128796953,2	MCF-7	breast:
5	chr12:62978537..62982109-chr12:62993246..62999032,10	MCF-7	breast:
6	chr12:62993534..62994890-chr12:63187464..63188240,4	MCF-7	breast:
7	chr1:155099354..155102099-chr12:62992358..62995047,2	MCF-7	breast:
8	chr12:62983638..62988242-chr12:62993831..62996165,4	K562	blood:
9	chr12:62993913..62996501-chr9:136325777..136327480,2	MCF-7	breast:

Variant related genes	Relation type
MIRLET7I	TF binding region
ENSG00000257354	TF binding region
ENSG00000061987	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000249421	Chromatin interaction
ENSG00000145808	Chromatin interaction
ENSG00000160325	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11174491	0.89[ASN][1000 genomes]
rs11174502	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11174503	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174515	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174531	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11174549	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174554	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174560	0.95[EUR][1000 genomes]
rs11174561	0.95[EUR][1000 genomes]
rs11174566	0.95[EUR][1000 genomes]
rs11174567	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11559995	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12161814	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12229932	0.87[EUR][1000 genomes]
rs3825305	0.81[EUR][1000 genomes]
rs4405369	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4494347	0.89[EUR][1000 genomes]
rs7302781	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74095806	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74095822	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	esv2558829	chr12:62992678-62994139	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62917200-62995000	Weak transcription	Fetal Heart	heart
2	chr12:62928800-62995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:62938000-62995400	Weak transcription	Stomach Mucosa	stomach
4	chr12:62950400-62995600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:62950600-62996200	Weak transcription	Small Intestine	intestine
6	chr12:62950800-62995000	Weak transcription	NHEK	skin
7	chr12:62951000-62995600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:62951200-62995200	Weak transcription	Hela-S3	cervix
9	chr12:62951200-62995600	Weak transcription	HSMMtube	muscle
10	chr12:62951400-62995000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:62953400-62996000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:62954800-62995600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:62955200-62995200	Weak transcription	HepG2	liver
14	chr12:62955600-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:62957000-62995600	Weak transcription	Fetal Brain Male	brain
16	chr12:62957200-62995600	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:62959600-62995600	Weak transcription	NHLF	lung
18	chr12:62961200-62995600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:62961400-62995600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr12:62961400-62995600	Weak transcription	Brain Germinal Matrix	brain
21	chr12:62961600-62995600	Weak transcription	Fetal Brain Female	brain
22	chr12:62961800-62995600	Weak transcription	Brain Substantia Nigra	brain
23	chr12:62962000-62995600	Weak transcription	HMEC	breast
24	chr12:62963200-62995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:62964000-62995800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:62966200-62995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:62966200-62995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:62966400-62995600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:62966400-62995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:62966600-62995600	Weak transcription	Thymus	Thymus
31	chr12:62966600-62996000	Weak transcription	Esophagus	oesophagus
32	chr12:62969000-62995600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:62969000-62996000	Weak transcription	Left Ventricle	heart
34	chr12:62969000-62996000	Weak transcription	Ovary	ovary
35	chr12:62970000-62995200	Weak transcription	Fetal Lung	lung
36	chr12:62978200-62995600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:62979200-62995600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:62980000-62995600	Weak transcription	Primary T cells from cord blood	blood
39	chr12:62980000-62995600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:62981000-62995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:62981000-62995400	Weak transcription	Dnd41	blood
42	chr12:62981000-62995600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr12:62981600-62996000	Weak transcription	Aorta	Aorta
44	chr12:62982000-62995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:62983000-62995600	Weak transcription	Fetal Thymus	thymus
46	chr12:62983200-62995600	Weak transcription	NH-A	brain
47	chr12:62983600-62995200	Weak transcription	Osteobl	bone
48	chr12:62983600-62995400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:62983600-62995600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:62983800-62995200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links