Variant report

Variant	rs11574952
Chromosome Location	chr12:46385815-46385816
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	POLR2A	chr12:46383410-46386164	Raji	blood:	n/a	n/a
2	POLR2A	chr12:46385297-46386185	GM12892	blood:	n/a	n/a
3	ZNF143	chr12:46385537-46385988	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr12:46385572-46386070	A549	lung:	n/a	n/a
5	CEBPB	chr12:46385787-46385990	HepG2	liver:	n/a	n/a
6	HDAC2	chr12:46385491-46386079	MCF-7	breast:	n/a	n/a
7	EGR1	chr12:46383831-46386188	HCT-116	colon:	n/a	chr12:46385601-46385612 chr12:46385599-46385613 chr12:46385599-46385614 chr12:46385601-46385610 chr12:46384692-46384701 chr12:46385600-46385613 chr12:46384634-46384658
8	EGR1	chr12:46385483-46385847	GM12878	blood:	n/a	chr12:46385601-46385612 chr12:46385599-46385613 chr12:46385599-46385614 chr12:46385601-46385610 chr12:46385600-46385613
9	MAFK	chr12:46385414-46386101	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr12:46384019-46386125	K562	blood:	n/a	n/a
11	STAT1	chr12:46384095-46386092	Hela-S3	cervix:	n/a	chr12:46384627-46384650 chr12:46384642-46384665 chr12:46384642-46384650 chr12:46384640-46384651 chr12:46385513-46385524
12	TBP	chr12:46385568-46385993	H1-hESC	embryonic stem cell:	n/a	n/a
13	MXI1	chr12:46383067-46386129	GM12878	blood:	n/a	n/a
14	HCFC1	chr12:46383104-46387294	Hela-S3	cervix:	n/a	n/a
15	ELK1	chr12:46385384-46386099	Hela-S3	cervix:	n/a	chr12:46385539-46385548 chr12:46385539-46385548
16	POU2F2	chr12:46385613-46385984	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:46385348-46386266	HEK293	kidney:	n/a	n/a
18	NR2F2	chr12:46384039-46386099	K562	blood:	n/a	n/a
19	SIN3AK20	chr12:46385676-46386072	A549	lung:	n/a	n/a
20	UBTF	chr12:46385466-46386033	K562	blood:	n/a	n/a
21	PAX5	chr12:46385399-46386028	GM12878	blood:	n/a	chr12:46385515-46385524
22	MAX	chr12:46385353-46386102	HepG2	liver:	n/a	n/a
23	HMGN3	chr12:46385204-46385998	K562	blood:	n/a	n/a
24	YY1	chr12:46385488-46385976	HCT-116	colon:	n/a	chr12:46385711-46385722
25	POLR2A	chr12:46383454-46386121	Hela-S3	cervix:	n/a	n/a
26	HEY1	chr12:46385409-46386079	K562	blood:	n/a	chr12:46385648-46385663
27	POU2F2	chr12:46385474-46386067	GM12891	blood:	n/a	n/a
28	TAF1	chr12:46385397-46386014	HepG2	liver:	n/a	n/a
29	MYC	chr12:46385796-46385936	HepG2	liver:	n/a	n/a
30	TBP	chr12:46385404-46386145	GM12878	blood:	n/a	n/a
31	HDAC2	chr12:46385480-46386013	HepG2	liver:	n/a	n/a
32	BCLAF1	chr12:46385461-46386197	GM12878	blood:	n/a	n/a
33	BACH1	chr12:46385543-46385944	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr12:46385742-46386000	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:46385350-46386188	GM12878	blood:	n/a	n/a
36	ARID3A	chr12:46385554-46386042	K562	blood:	n/a	n/a
37	RUNX3	chr12:46383321-46386244	GM12878	blood:	n/a	n/a
38	TCF3	chr12:46385547-46386044	GM12878	blood:	n/a	n/a
39	YY1	chr12:46385456-46386139	GM12878	blood:	n/a	chr12:46385711-46385722
40	YY1	chr12:46385390-46386124	GM12878	blood:	n/a	chr12:46385711-46385722
41	E2F6	chr12:46385475-46385971	K562	blood:	n/a	n/a
42	ARID3A	chr12:46385522-46385955	HepG2	liver:	n/a	n/a
43	TRIM28	chr12:46385316-46386182	K562	blood:	n/a	n/a
44	ATF3	chr12:46385498-46386054	A549	lung:	n/a	n/a
45	RFX5	chr12:46385451-46386186	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr12:46383331-46386125	GM12892	blood:	n/a	n/a
47	TBL1XR1	chr12:46385366-46386186	K562	blood:	n/a	n/a
48	TAF1	chr12:46385322-46386159	Hela-S3	cervix:	n/a	n/a
49	TAF1	chr12:46385490-46386100	GM12891	blood:	n/a	n/a
50	BCLAF1	chr12:46385350-46386090	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46381030..46386260-chr12:46762457..46768592,6	K562	blood:
2	chr12:46382717..46386243-chr12:46660668..46665434,7	MCF-7	breast:
3	chr12:46381426..46387093-chr12:46763754..46767064,8	MCF-7	breast:
4	chr12:46382760..46386151-chr12:46661620..46664692,5	K562	blood:
5	chr12:46385478..46386392-chr12:53298360..53298860,2	Hela-S3	cervix:
6	chr12:46382586..46387481-chr12:46763277..46769922,9	K562	blood:
7	chr12:46385410..46386104-chr6:89790440..89791393,2	Hela-S3	cervix:
8	chr12:46117578..46127110-chr12:46379884..46387671,22	K562	blood:
9	chr12:46119117..46128831-chr12:46378175..46388065,20	MCF-7	breast:
10	chr12:46382194..46387214-chr12:46392482..46398742,9	MCF-7	breast:
11	chr12:46383804..46386112-chr12:46763445..46766511,3	MCF-7	breast:
12	chr12:46385385..46385940-chrX:48455480..48456095,2	Hela-S3	cervix:
13	chr12:46385364..46385933-chr13:111365517..111366125,2	NB4	blood:
14	chr12:46385222..46385938-chr3:100053261..100054095,2	Hela-S3	cervix:
15	chr12:46383984..46386304-chr12:46660462..46663011,4	MCF-7	breast:
16	chr12:46385759..46386714-chr14:39735705..39736361,2	Hela-S3	cervix:
17	chr12:46383422..46386151-chr12:46661938..46664140,2	K562	blood:
18	chr12:46121418..46125188-chr12:46383049..46386096,7	MCF-7	breast:
19	chr12:46385525..46386462-chr12:109124486..109125310,2	Hela-S3	cervix:
20	chr12:45607714..45610119-chr12:46385742..46387348,2	K562	blood:
21	chr12:46119690..46125014-chr12:46381902..46386942,12	K562	blood:
22	chr12:46385180..46385828-chr12:51632634..51633506,2	Hela-S3	cervix:

Variant related genes	Relation type
SCAF11	TF binding region
ENSG00000153487	Chromatin interaction
ENSG00000146278	Chromatin interaction
ENSG00000258096	Chromatin interaction
ENSG00000110880	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000273015	Chromatin interaction
ENSG00000189079	Chromatin interaction
ENSG00000114021	Chromatin interaction
ENSG00000177119	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000101940	Chromatin interaction
ENSG00000239397	Chromatin interaction
ENSG00000111371	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000134297	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10748438	1.00[YRI][hapmap]
rs10880871	0.85[YRI][hapmap]
rs10880880	0.85[YRI][hapmap]
rs10880884	0.85[YRI][hapmap]
rs1366024	0.85[YRI][hapmap]
rs17096380	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7971398	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv983463	chr12:46377328-46403983	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 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	chr12:46380800-46386400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:46381200-46386200	Active TSS	Right Ventricle	heart
3	chr12:46381200-46386400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:46381200-46387200	Active TSS	GM12878-XiMat	blood
5	chr12:46381600-46386200	Active TSS	Psoas Muscle	Psoas
6	chr12:46382000-46386200	Active TSS	Aorta	Aorta
7	chr12:46382000-46386400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr12:46382000-46386400	Active TSS	NHLF	lung
9	chr12:46382200-46386200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr12:46382200-46386200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:46382200-46386200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:46382200-46386200	Active TSS	NHDF-Ad	bronchial
13	chr12:46382200-46386400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr12:46382200-46386400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr12:46382200-46386400	Active TSS	HSMMtube	muscle
16	chr12:46382400-46386000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:46382400-46386200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:46382400-46386200	Active TSS	HSMM	muscle
19	chr12:46382400-46386400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:46382400-46386400	Active TSS	A549	lung
21	chr12:46382400-46386600	Active TSS	K562	blood
22	chr12:46382800-46386000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr12:46382800-46386200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:46382800-46386200	Active TSS	Fetal Stomach	stomach
25	chr12:46383000-46386000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr12:46383000-46386000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:46383000-46386000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr12:46383000-46386000	Active TSS	Brain Angular Gyrus	brain
29	chr12:46383000-46386000	Active TSS	Brain Cingulate Gyrus	brain
30	chr12:46383000-46386000	Bivalent/Poised TSS	HepG2	liver
31	chr12:46383000-46386000	Active TSS	Osteobl	bone
32	chr12:46383000-46386200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr12:46383000-46386200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:46383000-46386200	Active TSS	Muscle Satellite Cultured Cells	--
35	chr12:46383000-46386200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:46383000-46386200	Active TSS	Colonic Mucosa	Colon
37	chr12:46383000-46386200	Active TSS	Fetal Brain Female	brain
38	chr12:46383000-46386200	Active TSS	Fetal Intestine Small	intestine
39	chr12:46383000-46386200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:46383000-46386200	Active TSS	Placenta	Placenta
41	chr12:46383000-46386200	Active TSS	Fetal Thymus	thymus
42	chr12:46383000-46386200	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr12:46383000-46386400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:46383000-46386400	Active TSS	Brain Anterior Caudate	brain
45	chr12:46383000-46386400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:46383000-46386400	Active TSS	Fetal Heart	heart
47	chr12:46383000-46386400	Active TSS	Fetal Intestine Large	intestine
48	chr12:46383200-46386000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:46383200-46386000	Active TSS	Lung	lung
50	chr12:46383200-46386000	Active TSS	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links