Variant report

Variant	rs12951323
Chromosome Location	chr17:46027565-46027566
allele	A/C
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	NFIC	chr17:46027215-46027581	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:46025886-46028079	HepG2	liver:	n/a	n/a
3	STAT5A	chr17:46026517-46027627	GM12878	blood:	n/a	n/a
4	USF2	chr17:46027366-46027664	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:46027469-46027669	MCF10A-Er-Src	breast:	n/a	n/a
6	RUNX3	chr17:46027358-46027650	GM12878	blood:	n/a	n/a
7	ELF1	chr17:46025871-46027669	MCF-7	breast:	n/a	chr17:46027412-46027423
8	MAX	chr17:46025916-46027747	MCF-7	breast:	n/a	n/a
9	EBF1	chr17:46026634-46027742	GM12878	blood:	n/a	chr17:46027577-46027588
10	POLR2A	chr17:46025953-46027582	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr17:46025867-46027977	MCF-7	breast:	n/a	n/a
12	RELA	chr17:46026694-46027592	GM18951	blood:	n/a	n/a
13	CTCF	chr17:46027500-46027790	Caco-2	colon:	n/a	n/a
14	EP300	chr17:46026710-46027666	GM12878	blood:	n/a	n/a
15	RAD21	chr17:46026095-46027764	SK-N-SH	brain:	n/a	chr17:46026780-46026799
16	CUX1	chr17:46027305-46027568	GM12878	blood:	n/a	n/a
17	RUNX3	chr17:46027224-46027615	GM12878	blood:	n/a	n/a
18	EBF1	chr17:46027355-46027710	GM12878	blood:	n/a	chr17:46027577-46027588
19	MTA3	chr17:46026386-46027751	GM12878	blood:	n/a	n/a
20	SMC3	chr17:46025869-46027855	SK-N-SH	brain:	n/a	chr17:46026781-46026795
21	CTCF	chr17:46025931-46027875	A549	lung:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
22	POLR2A	chr17:46025923-46028067	HepG2	liver:	n/a	n/a
23	CTCF	chr17:46025857-46027841	SK-N-SH	brain:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
24	FOSL2	chr17:46025826-46027645	A549	lung:	n/a	n/a
25	PML	chr17:46025834-46027617	MCF-7	breast:	n/a	n/a
26	CTCF	chr17:46027440-46027590	GM12871	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46026192..46029068-chr17:46087372..46089166,2	K562	blood:
2	chr17:45970281..45975378-chr17:46022719..46027732,11	MCF-7	breast:
3	chr17:46026023..46027620-chr17:46047369..46048630,14	MCF-7	breast:
4	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
5	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
6	chr17:46026764..46027682-chr17:46095633..46096284,2	MCF-7	breast:
7	chr17:46027110..46029262-chr17:46094448..46097370,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264019	TF binding region
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11650615	1.00[JPT][hapmap]
rs16952265	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1986693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41336845	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs4794321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823509	0.95[EUR][1000 genomes]
rs72823513	0.95[EUR][1000 genomes]
rs8073371	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs8076196	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
3	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
5	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:46025400-46027600	Genic enhancers	HMEC	breast
7	chr17:46025800-46027600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:46026000-46027600	Enhancers	Fetal Heart	heart
9	chr17:46026000-46027800	Enhancers	Primary B cells from cord blood	blood
10	chr17:46026000-46028000	Enhancers	Esophagus	oesophagus
11	chr17:46026200-46027600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr17:46026200-46027600	Enhancers	Left Ventricle	heart
13	chr17:46026200-46027600	Enhancers	Ovary	ovary
14	chr17:46026200-46027800	Enhancers	Primary B cells from peripheral blood	blood
15	chr17:46026200-46028000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
16	chr17:46026400-46027600	Flanking Active TSS	Liver	Liver
17	chr17:46026400-46027600	Enhancers	Dnd41	blood
18	chr17:46026400-46027600	Flanking Active TSS	GM12878-XiMat	blood
19	chr17:46026400-46027600	Enhancers	HSMM	muscle
20	chr17:46026400-46028000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:46026400-46028000	Enhancers	Placenta	Placenta
22	chr17:46026600-46027600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr17:46026600-46027600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
24	chr17:46026600-46027800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:46026800-46027600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:46026800-46027600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr17:46026800-46027600	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr17:46026800-46027600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
29	chr17:46026800-46027800	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
30	chr17:46026800-46027800	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
31	chr17:46027000-46027600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:46027000-46027600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:46027000-46027600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:46027000-46027600	Enhancers	Fetal Muscle Leg	muscle
35	chr17:46027000-46027600	Flanking Active TSS	Pancreas	Pancrea
36	chr17:46027000-46027800	Enhancers	Small Intestine	intestine
37	chr17:46027000-46028000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr17:46027000-46030000	Weak transcription	Psoas Muscle	Psoas
39	chr17:46027200-46027600	Enhancers	H1 Cell Line	embryonic stem cell
40	chr17:46027200-46027600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:46027200-46027600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
42	chr17:46027200-46027600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr17:46027200-46027600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
44	chr17:46027200-46027600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr17:46027200-46027600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr17:46027200-46027600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:46027200-46027600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:46027200-46027600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:46027200-46027600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:46027200-46027600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links