Variant report

Variant	rs538394
Chromosome Location	chr11:65630698-65630699
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65630365-65633811	ProgFib	skin:	n/a	n/a
2	POLR2A	chr11:65617092-65633870	K562	blood:	n/a	n/a
3	POLR2A	chr11:65630140-65633694	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:65630457-65632250	K562	blood:	n/a	n/a
5	POLR2A	chr11:65630290-65631180	K562	blood:	n/a	n/a
6	POLR2A	chr11:65630665-65630873	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:65616755-65639999	U87	brain:	n/a	n/a
8	POLR2A	chr11:65630460-65631188	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr11:65630406-65632402	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:65629110-65633804	K562	blood:	n/a	n/a
11	POLR2A	chr11:65630217-65632301	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr11:65616706-65640269	U87	brain:	n/a	n/a
13	POLR2A	chr11:65630667-65631382	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:65629647-65631226	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr11:65630584-65631042	GM12891	blood:	n/a	n/a
16	POLR2A	chr11:65630581-65631344	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:65630697-65630725	HUVEC	blood vessel:	n/a	n/a
18	HEY1	chr11:65630285-65631216	K562	blood:	n/a	n/a
19	POLR2A	chr11:65616501-65633874	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:65630574-65632265	GM12892	blood:	n/a	n/a
21	POLR2A	chr11:65630580-65631340	U87	brain:	n/a	n/a
22	POLR2A	chr11:65630570-65631340	U87	brain:	n/a	n/a
23	POLR2A	chr11:65630692-65630777	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:65630265-65633866	GM12892	blood:	n/a	n/a
25	POLR2A	chr11:65630461-65632067	PANC-1	pancreas:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65630101..65632052-chr11:65668031..65671023,2	MCF-7	breast:
2	chr11:65622510..65630779-chr11:65675126..65689187,23	MCF-7	breast:
3	chr11:65626619..65631270-chr11:65726316..65731782,7	MCF-7	breast:
4	chr11:65629227..65631870-chr11:65766567..65769342,2	MCF-7	breast:
5	chr11:65544951..65562337-chr11:65623093..65630859,34	MCF-7	breast:

No data

Variant related genes	Relation type
CFL1	TF binding region
MUS81	TF binding region
ENSG00000254470	Chromatin interaction
ENSG00000172818	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000175827	Chromatin interaction
ENSG00000255120	Chromatin interaction
ENSG00000175592	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10791828	0.81[CEU][hapmap];0.85[AMR][1000 genomes]
rs13817	0.92[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939212	0.81[CEU][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4621	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508548	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545500	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs558114	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630303	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630755	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs633877	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635375	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648732	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652021	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656040	0.92[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659857	0.96[CEU][hapmap]
rs665306	0.96[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667555	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs668356	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679147	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7125986	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7947741	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7947929	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
9	nsv897763	chr11:65613348-65644027	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	121 gene(s)	inside rSNPs	diseases
10	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
11	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
12	nsv897766	chr11:65624025-65644027	Transcr. at gene 5' and 3' Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs538394	FIBP	Cis_1M	lymphoblastoid	RTeQTL
rs538394	SNX32	cis	Whole Blood	GTEx
rs538394	SNX32	cis	Thyroid	GTEx
rs538394	SNX32	cis	Esophagus Muscularis	GTEx
rs538394	SNX32	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65628200-65633600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr11:65628800-65639600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:65629000-65631000	Genic enhancers	Fetal Thymus	thymus
4	chr11:65629000-65631600	Genic enhancers	Spleen	Spleen
5	chr11:65629000-65632600	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr11:65629000-65639600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:65629200-65630800	Genic enhancers	Colon Smooth Muscle	Colon
8	chr11:65629200-65631000	Genic enhancers	Adipose Nuclei	Adipose
9	chr11:65629200-65631000	Genic enhancers	Brain Inferior Temporal Lobe	brain
10	chr11:65629200-65631200	Genic enhancers	Right Ventricle	heart
11	chr11:65629200-65631600	Genic enhancers	Fetal Stomach	stomach
12	chr11:65629200-65632800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:65629200-65634600	Strong transcription	Aorta	Aorta
14	chr11:65629400-65631000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
15	chr11:65629400-65631000	Weak transcription	Small Intestine	intestine
16	chr11:65629400-65631200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr11:65629400-65631600	Weak transcription	Fetal Kidney	kidney
18	chr11:65629400-65631800	Enhancers	Fetal Heart	heart
19	chr11:65629400-65632600	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr11:65629400-65633200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:65629400-65634400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:65629400-65634400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:65629400-65634800	Strong transcription	Brain Substantia Nigra	brain
24	chr11:65629400-65635200	Strong transcription	Brain Anterior Caudate	brain
25	chr11:65629400-65638600	Weak transcription	Right Atrium	heart
26	chr11:65629600-65630800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:65629600-65630800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:65629600-65630800	Genic enhancers	Duodenum Mucosa	Duodenum
29	chr11:65629600-65631000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:65629600-65631600	Weak transcription	HSMM	muscle
31	chr11:65629600-65631800	Genic enhancers	Rectal Mucosa Donor 29	rectum
32	chr11:65629600-65633400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr11:65629600-65633400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:65629600-65633600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:65629600-65633600	Strong transcription	Brain Angular Gyrus	brain
36	chr11:65629600-65633800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:65629600-65634400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr11:65629600-65634400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:65629600-65634600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr11:65629600-65634800	Strong transcription	Primary T cells from cord blood	blood
41	chr11:65629600-65635000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:65629600-65635000	Strong transcription	Esophagus	oesophagus
43	chr11:65629600-65635400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:65629600-65635600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:65629600-65635800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:65629600-65636000	Strong transcription	Thymus	Thymus
47	chr11:65629600-65637400	Strong transcription	Ovary	ovary
48	chr11:65629600-65637600	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr11:65629600-65638000	Strong transcription	Fetal Lung	lung
50	chr11:65629800-65630800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links