Variant report

Variant	rs9579412
Chromosome Location	chr13:30163781-30163782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr13:30163698-30163859	MCF-7	breast:	n/a	n/a
2	FOXM1	chr13:30163096-30163817	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr13:30163693-30163874	MCF-7	breast:	n/a	n/a
4	TCF12	chr13:30163333-30163967	SK-N-SH	brain:	n/a	chr13:30163646-30163656
5	POLR2A	chr13:30163758-30164355	GM12892	blood:	n/a	n/a
6	TEAD4	chr13:30163296-30163939	ECC-1	luminal epithelium:	n/a	n/a
7	TCF12	chr13:30163088-30164317	ECC-1	luminal epithelium:	n/a	chr13:30163136-30163146 chr13:30163646-30163656
8	TEAD4	chr13:30163287-30163884	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr13:30163316-30163945	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr13:30163684-30163895	MCF-7	breast:	n/a	n/a
11	POLR2A	chr13:30163687-30163956	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr13:30163081-30164741	HepG2	liver:	n/a	n/a
13	RAD21	chr13:30163379-30163998	ECC-1	luminal epithelium:	n/a	n/a
14	MYC	chr13:30163725-30163806	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr13:30163177-30164135	GM12892	blood:	n/a	n/a
16	POLR2A	chr13:30163287-30164938	GM12878	blood:	n/a	n/a
17	POLR2A	chr13:30163296-30163924	ECC-1	luminal epithelium:	n/a	n/a
18	PBX3	chr13:30163208-30163835	SK-N-SH	brain:	n/a	n/a
19	NFIC	chr13:30163146-30164030	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr13:30163746-30163881	MCF-7	breast:	n/a	n/a
21	NFIC	chr13:30163169-30163971	ECC-1	luminal epithelium:	n/a	n/a
22	ESR1	chr13:30163255-30163951	ECC-1	luminal epithelium:	n/a	n/a
23	ESR1	chr13:30163231-30163987	ECC-1	luminal epithelium:	n/a	n/a
24	ESR1	chr13:30163211-30163943	ECC-1	luminal epithelium:	n/a	n/a
25	FOXM1	chr13:30163128-30164080	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr13:30163436-30163810	K562	blood:	n/a	n/a
27	TCF12	chr13:30163119-30164269	ECC-1	luminal epithelium:	n/a	chr13:30163136-30163146 chr13:30163646-30163656
28	EP300	chr13:30163188-30163975	ECC-1	luminal epithelium:	n/a	n/a
29	CTCF	chr13:30163680-30163879	NHEK	skin:	n/a	n/a
30	POLR2A	chr13:30163104-30164866	Hela-S3	cervix:	n/a	n/a
31	EP300	chr13:30163012-30164336	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr13:30163676-30164035	GM12878	blood:	n/a	n/a
33	ZBTB7A	chr13:30163207-30163964	ECC-1	luminal epithelium:	n/a	n/a
34	TCF12	chr13:30163209-30164016	SK-N-SH	brain:	n/a	chr13:30163646-30163656
35	CTCF	chr13:30163700-30163850	RPTEC	kidney:	n/a	n/a
36	ZBTB7A	chr13:30163124-30164013	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr13:30163580-30164336	A549	lung:	n/a	n/a
38	POLR2A	chr13:30162982-30164138	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr13:30163391-30163931	ECC-1	luminal epithelium:	n/a	n/a
40	CTCF	chr13:30163747-30163816	MCF-7	breast:	n/a	n/a
41	POLR2A	chr13:30163496-30163917	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30163424..30165091-chr13:31039254..31040913,2	K562	blood:
2	chr13:30142261..30144231-chr13:30163491..30165148,2	MCF-7	breast:

No data

Variant related genes	Relation type
SLC7A1	TF binding region
ENSG00000189403	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs280918	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280919	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56853211	0.94[ASN][1000 genomes]
rs7318650	0.94[ASN][1000 genomes]
rs7981502	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002439	0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv979	chr13:30122254-30167821	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30128800-30168200	Weak transcription	Primary T cells from cord blood	blood
2	chr13:30148400-30167400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr13:30152600-30168200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:30156400-30164000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:30156400-30168400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr13:30156600-30164000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:30156800-30168200	Weak transcription	Fetal Brain Female	brain
8	chr13:30156800-30168400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr13:30157000-30164000	Weak transcription	Brain Hippocampus Middle	brain
10	chr13:30157200-30168400	Weak transcription	Brain Germinal Matrix	brain
11	chr13:30157600-30163800	Weak transcription	Right Atrium	heart
12	chr13:30157600-30166000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr13:30157600-30168200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr13:30157600-30168200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:30157800-30166400	Weak transcription	Lung	lung
16	chr13:30157800-30168200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:30157800-30168400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr13:30157800-30168400	Weak transcription	Small Intestine	intestine
19	chr13:30157800-30168600	Weak transcription	Ovary	ovary
20	chr13:30158000-30168600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr13:30158200-30166800	Weak transcription	Fetal Thymus	thymus
22	chr13:30158200-30168400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr13:30158800-30165600	Weak transcription	A549	lung
24	chr13:30159400-30165800	Weak transcription	K562	blood
25	chr13:30159400-30168200	Weak transcription	Brain Angular Gyrus	brain
26	chr13:30159600-30164000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:30159600-30164200	Weak transcription	Fetal Brain Male	brain
28	chr13:30159800-30165600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr13:30160000-30164000	Weak transcription	Hela-S3	cervix
30	chr13:30160000-30167400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:30160000-30168400	Weak transcription	Psoas Muscle	Psoas
32	chr13:30160200-30164400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr13:30160200-30167000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr13:30160800-30165400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr13:30161000-30164000	Strong transcription	Fetal Stomach	stomach
36	chr13:30161400-30164000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr13:30161400-30164400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:30161400-30165400	Genic enhancers	Osteobl	bone
39	chr13:30161400-30167400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:30161600-30165400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:30161600-30165600	Weak transcription	HUVEC	blood vessel
42	chr13:30161800-30164000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:30161800-30164200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr13:30161800-30164400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr13:30161800-30164400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:30161800-30164800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr13:30162000-30165200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:30162000-30168400	Weak transcription	Aorta	Aorta
49	chr13:30162200-30164000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:30162200-30168400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links