Variant report

Variant	rs11171667
Chromosome Location	chr12:56131052-56131053
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:228)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:228 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:56130844-56131349	H1-hESC	embryonic stem cell:	n/a	chr12:56131304-56131316
2	YY1	chr12:56130956-56131137	HCT-116	colon:	n/a	n/a
3	CTCF	chr12:56130900-56131294	MCF-7	breast:	n/a	n/a
4	CTCF	chr12:56131019-56131281	GM20000	blood:	n/a	n/a
5	CTCF	chr12:56130946-56131316	Kidney_OC	kidney:	n/a	n/a
6	MAFF	chr12:56130940-56131293	K562	blood:	n/a	n/a
7	YY1	chr12:56130923-56131263	HCT-116	colon:	n/a	n/a
8	MAX	chr12:56130950-56131246	Hela-S3	cervix:	n/a	n/a
9	TEAD4	chr12:56130896-56131331	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFK	chr12:56130907-56131302	H1-hESC	embryonic stem cell:	n/a	n/a
11	ARID3A	chr12:56130903-56131302	HepG2	liver:	n/a	n/a
12	MAX	chr12:56131009-56131273	NB4	blood:	n/a	n/a
13	BACH1	chr12:56130982-56131144	K562	blood:	n/a	n/a
14	RAD21	chr12:56130938-56131316	A549	lung:	n/a	chr12:56131304-56131316
15	SP1	chr12:56130838-56131342	H1-hESC	embryonic stem cell:	n/a	chr12:56131251-56131265
16	RAD21	chr12:56130723-56131439	H1-hESC	embryonic stem cell:	n/a	chr12:56131304-56131316
17	ZNF384	chr12:56131032-56131223	K562	blood:	n/a	n/a
18	CTCF	chr12:56130890-56131314	MCF-7	breast:	n/a	n/a
19	CTCF	chr12:56131020-56131170	Caco-2	colon:	n/a	n/a
20	MAX	chr12:56130806-56131375	H1-hESC	embryonic stem cell:	n/a	n/a
21	CHD2	chr12:56130911-56131129	Hela-S3	cervix:	n/a	n/a
22	SMC3	chr12:56130924-56131378	GM12878	blood:	n/a	n/a
23	RAD21	chr12:56130777-56131272	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr12:56130591-56131852	HCT-116	colon:	n/a	n/a
25	RAD21	chr12:56130703-56133189	SK-N-SH	brain:	n/a	chr12:56132751-56132770 chr12:56131745-56131757 chr12:56131304-56131316
26	CTCF	chr12:56130934-56131313	Gliobla	brain:	n/a	n/a
27	CTCF	chr12:56131040-56131190	SAEC	small airway:	n/a	n/a
28	EP300	chr12:56130829-56131333	H1-hESC	embryonic stem cell:	n/a	n/a
29	TEAD4	chr12:56130785-56131290	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr12:56130899-56131298	HCT-116	colon:	n/a	n/a
31	CTCF	chr12:56130871-56131369	K562	blood:	n/a	n/a
32	MAX	chr12:56130897-56131284	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr12:56130932-56131312	K562	blood:	n/a	n/a
34	RAD21	chr12:56130877-56131366	HepG2	liver:	n/a	chr12:56131304-56131316
35	CTCF	chr12:56131000-56131150	WERI-Rb-1	eye:	n/a	n/a
36	ZNF143	chr12:56131000-56131321	K562	blood:	n/a	n/a
37	BACH1	chr12:56130868-56131320	H1-hESC	embryonic stem cell:	n/a	n/a
38	TBL1XR1	chr12:56131002-56131242	K562	blood:	n/a	n/a
39	CTCF	chr12:56131040-56131190	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr12:56131040-56131190	HFF-Myc	foreskin:	n/a	n/a
41	YY1	chr12:56130901-56131294	A549	lung:	n/a	n/a
42	CTCF	chr12:56130816-56131384	H1-hESC	embryonic stem cell:	n/a	n/a
43	BHLHE40	chr12:56131005-56131300	K562	blood:	n/a	n/a
44	KAP1	chr12:56130893-56131227	U2OS	brain:	n/a	n/a
45	ZNF143	chr12:56130860-56131336	H1-hESC	embryonic stem cell:	n/a	n/a
46	FOXM1	chr12:56130921-56131386	GM12878	blood:	n/a	n/a
47	CTCF	chr12:56131040-56131190	HL-60	blood:	n/a	n/a
48	RCOR1	chr12:56130914-56131341	K562	blood:	n/a	n/a
49	BRCA1	chr12:56130944-56131207	HepG2	liver:	n/a	n/a
50	CREB1	chr12:56130762-56131372	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56130509..56134677-chr12:56319153..56322835,6	MCF-7	breast:
2	chr12:56128209..56131175-chr12:56191287..56192790,2	MCF-7	breast:
3	chr12:56126382..56129342-chr12:56130269..56131927,2	K562	blood:
4	chr12:56129754..56132274-chr12:56222325..56224996,4	MCF-7	breast:
5	chr12:56130516..56133996-chr12:56433769..56437389,4	MCF-7	breast:
6	chr12:56114749..56115344-chr12:56130680..56131551,3	MCF-7	breast:
7	chr12:56128491..56132678-chr12:56134367..56139397,6	MCF-7	breast:
8	chr12:56129313..56132874-chr12:56186006..56190990,5	MCF-7	breast:
9	chr12:56130066..56132507-chr12:56399806..56401783,2	MCF-7	breast:
10	chr12:56052581..56055368-chr12:56130913..56132507,2	MCF-7	breast:
11	chr12:56130822..56132670-chr12:56222783..56225196,2	K562	blood:
12	chr12:56118355..56119078-chr12:56130717..56131614,5	K562	blood:
13	chr12:56130904..56133649-chr12:56685067..56686704,2	MCF-7	breast:
14	chr12:56118190..56119080-chr12:56130780..56131563,6	MCF-7	breast:
15	chr12:56126768..56128465-chr12:56130019..56132684,2	K562	blood:
16	chr12:56053176..56054498-chr12:56130542..56131569,11	MCF-7	breast:
17	chr12:56129997..56132260-chr12:56208494..56211865,3	MCF-7	breast:
18	chr12:56131041..56132670-chr12:56349196..56352159,2	MCF-7	breast:
19	chr12:56093666..56095175-chr12:56129843..56132682,2	MCF-7	breast:
20	chr12:56118075..56119434-chr12:56130540..56132004,12	MCF-7	breast:
21	chr12:56130927..56134179-chr12:56510145..56513079,3	MCF-7	breast:
22	chr12:56074581..56075906-chr12:56130550..56131834,8	MCF-7	breast:
23	chr12:56074134..56076898-chr12:56129940..56132449,2	MCF-7	breast:
24	chr12:56128998..56134444-chr12:56209748..56213922,6	MCF-7	breast:
25	chr12:56074901..56075515-chr12:56130637..56131479,4	MCF-7	breast:
26	chr12:56121828..56122420-chr12:56130741..56131437,2	MCF-7	breast:
27	chr12:56130710..56134380-chr12:56135389..56139193,10	MCF-7	breast:
28	chr12:56126940..56128624-chr12:56129633..56132627,3	MCF-7	breast:
29	chr12:56129813..56131866-chr12:56367463..56370403,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257384	TF binding region
ENSG00000229117	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000257384	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000123411	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000135437	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000258921	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10082864	0.82[EUR][1000 genomes]
rs10083186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[EUR][1000 genomes]
rs10161417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs11171670	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171671	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes]
rs11171681	0.91[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11829536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11834264	0.97[EUR][1000 genomes]
rs12304296	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12304507	0.82[EUR][1000 genomes]
rs12320756	0.97[EUR][1000 genomes]
rs17117974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2291267	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3759101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7297523	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7299222	0.94[EUR][1000 genomes]
rs7971247	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7972345	0.82[EUR][1000 genomes]
rs868051	0.97[EUR][1000 genomes]
rs9739244	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[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	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56124000-56131200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56124400-56131600	Weak transcription	Gastric	stomach
3	chr12:56124600-56131600	Weak transcription	Spleen	Spleen
4	chr12:56124600-56131800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:56124600-56131800	Weak transcription	NHEK	skin
6	chr12:56124800-56131400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:56125000-56131200	Weak transcription	Osteobl	bone
8	chr12:56125000-56132200	Weak transcription	Lung	lung
9	chr12:56125600-56131200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:56126600-56131600	Weak transcription	Pancreas	Pancrea
11	chr12:56127200-56136000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:56129800-56131400	Enhancers	Brain Germinal Matrix	brain
13	chr12:56129800-56131600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr12:56129800-56131600	Enhancers	Fetal Muscle Trunk	muscle
15	chr12:56129800-56131800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr12:56129800-56131800	Enhancers	Fetal Intestine Small	intestine
17	chr12:56130000-56131200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:56130000-56131400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:56130000-56131400	Enhancers	Fetal Thymus	thymus
20	chr12:56130000-56131800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr12:56130000-56132000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:56130200-56131200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr12:56130200-56131200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr12:56130200-56131400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:56130200-56131600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:56130200-56131600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:56130200-56131800	Enhancers	Fetal Heart	heart
28	chr12:56130400-56131200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr12:56130400-56131400	Enhancers	Fetal Stomach	stomach
30	chr12:56130400-56131800	Enhancers	Fetal Intestine Large	intestine
31	chr12:56130400-56132400	Enhancers	Right Ventricle	heart
32	chr12:56130400-56132600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:56130600-56131200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:56130600-56131200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:56130600-56131200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr12:56130600-56131400	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:56130600-56131400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:56130600-56131400	Enhancers	Fetal Lung	lung
39	chr12:56130600-56131600	Enhancers	H1 Cell Line	embryonic stem cell
40	chr12:56130600-56131600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:56130600-56131600	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:56130600-56131600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:56130600-56131600	Enhancers	Fetal Muscle Leg	muscle
44	chr12:56130600-56131600	Enhancers	Stomach Smooth Muscle	stomach
45	chr12:56130600-56131800	Enhancers	Primary hematopoietic stem cells	blood
46	chr12:56130600-56131800	Enhancers	Brain Substantia Nigra	brain
47	chr12:56130600-56131800	Enhancers	Fetal Brain Male	brain
48	chr12:56130600-56131800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:56130600-56132000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:56130600-56132000	Enhancers	Placenta	Placenta

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