Variant report

Variant	rs633800
Chromosome Location	chr11:65638719-65638720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65631446-65639140	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr11:65636346-65639953	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr11:65616755-65639999	U87	brain:	n/a	n/a
4	MAX	chr11:65637990-65638744	NB4	blood:	n/a	n/a
5	POLR2A	chr11:65638632-65638753	A549	lung:	n/a	n/a
6	POLR2A	chr11:65638707-65638742	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:65637924-65638725	GM12891	blood:	n/a	n/a
8	POLR2A	chr11:65634816-65638944	GM12891	blood:	n/a	n/a
9	POLR2A	chr11:65635498-65638874	U87	brain:	n/a	n/a
10	POLR2A	chr11:65633881-65638811	GM12892	blood:	n/a	n/a
11	POLR2A	chr11:65616706-65640269	U87	brain:	n/a	n/a
12	NFATC1	chr11:65635820-65638736	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:65637649-65638770	ProgFib	skin:	n/a	n/a
14	POLR2A	chr11:65633886-65639510	K562	blood:	n/a	n/a
15	POLR2A	chr11:65635498-65638868	U87	brain:	n/a	n/a
16	POLR2A	chr11:65638636-65638806	MCF-7	breast:	n/a	n/a
17	POLR2A	chr11:65637023-65638873	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr11:65635163-65639373	GM12891	blood:	n/a	n/a
19	MAZ	chr11:65638665-65641701	IMR90	lung:	n/a	chr11:65639908-65639918 chr11:65640385-65640395 chr11:65640115-65640124
20	POU2F2	chr11:65638034-65638742	GM12891	blood:	n/a	n/a
21	POLR2A	chr11:65636912-65639982	K562	blood:	n/a	n/a
22	POLR2A	chr11:65633945-65638829	HepG2	liver:	n/a	n/a
23	POLR2A	chr11:65635223-65639302	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:65636785-65639990	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:65633979-65640025	GM12892	blood:	n/a	n/a
26	POLR2A	chr11:65634001-65639492	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr11:65638448-65638800	GM12891	blood:	n/a	n/a
28	POLR2A	chr11:65635289-65639598	GM12878	blood:	n/a	n/a
29	POLR2A	chr11:65637963-65638861	Hela-S3	cervix:	n/a	n/a
30	MYC	chr11:65638098-65638771	NB4	blood:	n/a	n/a
31	POLR2A	chr11:65633858-65638833	K562	blood:	n/a	n/a
32	POLR2A	chr11:65633995-65639964	GM12892	blood:	n/a	n/a
33	POLR2A	chr11:65633880-65639155	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:65638297-65639227	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65477979..65480813-chr11:65636240..65639820,3	K562	blood:
2	chr11:65478490..65481819-chr11:65637441..65641209,4	K562	blood:
3	chr11:65636578..65639381-chr11:65766938..65769474,2	MCF-7	breast:
4	chr11:65638377..65641229-chr11:65727913..65730693,2	MCF-7	breast:

No data

Variant related genes	Relation type
EFEMP2	TF binding region
ENSG00000175467	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000172977	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10750772	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10791827	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10896047	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10896051	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10896052	0.90[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10896061	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10896064	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227309	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11227311	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11227312	0.86[AMR][1000 genomes]
rs11227318	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11602769	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12575663	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12576996	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs13817	0.82[GIH][hapmap]
rs3892696	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap]
rs3903072	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs485036	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.80[ASN][1000 genomes]
rs4930320	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4930326	0.87[AMR][1000 genomes]
rs501630	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs558114	0.80[GIH][hapmap]
rs566266	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs570387	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs594689	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630303	0.80[GIH][hapmap]
rs635375	0.80[GIH][hapmap]
rs648732	0.80[GIH][hapmap]
rs652021	0.80[GIH][hapmap]
rs656040	0.82[GIH][hapmap]
rs659824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs659857	0.80[GIH][hapmap]
rs665306	0.80[GIH][hapmap]
rs668356	0.80[GIH][hapmap]
rs674126	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs7107912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7123155	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs875311	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
13	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
14	esv999644	chr11:65636167-65646034	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	esv1797198	chr11:65637273-65642343	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs633800	PRDX5	cis	parietal	SCAN
rs633800	SNX32	cis	Thyroid	GTEx
rs633800	RAB1B	cis	cerebellum	SCAN
rs633800	SART1	cis	parietal	SCAN
rs633800	EFEMP2	cis	cerebellum	SCAN
rs633800	SNX32	cis	cerebellum	SCAN
rs633800	SNX32	cis	parietal	SCAN
rs633800	CARNS1	cis	cerebellum	SCAN
rs633800	PACS1	cis	parietal	SCAN
rs633800	PLCB3	cis	parietal	SCAN
rs633800	LRRN4CL	cis	cerebellum	SCAN
rs633800	EIF1AD	cis	parietal	SCAN
rs633800	SNX32	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65628800-65639600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:65629000-65639600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:65632200-65639400	Weak transcription	Fetal Kidney	kidney
4	chr11:65633000-65639400	Weak transcription	Psoas Muscle	Psoas
5	chr11:65633200-65639200	Weak transcription	Stomach Mucosa	stomach
6	chr11:65633400-65640600	Weak transcription	Hela-S3	cervix
7	chr11:65633600-65639400	Weak transcription	Brain Angular Gyrus	brain
8	chr11:65633600-65640400	Weak transcription	HMEC	breast
9	chr11:65633800-65639200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:65634400-65638800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:65634400-65639600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:65634800-65639200	Weak transcription	Brain Substantia Nigra	brain
13	chr11:65634800-65639600	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:65634800-65640400	Weak transcription	Primary T cells from cord blood	blood
15	chr11:65635000-65639800	Weak transcription	Small Intestine	intestine
16	chr11:65635000-65640000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:65635200-65639200	Weak transcription	Brain Anterior Caudate	brain
18	chr11:65635200-65640400	Weak transcription	Dnd41	blood
19	chr11:65635600-65639000	Weak transcription	Brain Germinal Matrix	brain
20	chr11:65635600-65639600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:65635600-65640600	Weak transcription	K562	blood
22	chr11:65635800-65639200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:65635800-65639200	Weak transcription	Fetal Brain Female	brain
24	chr11:65635800-65639200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:65635800-65640600	Weak transcription	A549	lung
26	chr11:65636000-65638800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:65636000-65638800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:65636000-65639200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:65636000-65639200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:65636000-65639200	Weak transcription	Fetal Brain Male	brain
31	chr11:65636000-65639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:65636200-65639400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:65636200-65640400	Weak transcription	NHEK	skin
34	chr11:65636600-65639200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:65636600-65639400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:65637000-65639000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:65637000-65639800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:65637200-65638800	Genic enhancers	Spleen	Spleen
39	chr11:65637200-65639000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:65637200-65639400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:65637200-65640200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:65637400-65638800	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr11:65637400-65639000	Genic enhancers	Fetal Stomach	stomach
44	chr11:65637400-65640400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:65637600-65638800	Weak transcription	HSMMtube	muscle
46	chr11:65637600-65639000	Enhancers	Liver	Liver
47	chr11:65637600-65639000	Enhancers	Duodenum Mucosa	Duodenum
48	chr11:65637600-65639000	Enhancers	Fetal Heart	heart
49	chr11:65637600-65639000	Genic enhancers	Right Ventricle	heart
50	chr11:65637600-65639000	Enhancers	Skeletal Muscle Female	skeletal muscle

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