Variant report

Variant	rs2448490
Chromosome Location	chr11:65412035-65412036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65412030-65412505	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:65410580-65415232	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:65411875-65412097	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:65411021-65412367	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65381837..65384874-chr11:65408944..65413829,9	MCF-7	breast:
2	chr11:65394604..65399186-chr11:65411487..65416339,5	MCF-7	breast:
3	chr11:65353979..65355794-chr11:65410374..65412604,2	MCF-7	breast:
4	chr11:64851522..64853980-chr11:65411333..65413797,2	K562	blood:
5	chr11:65386206..65389364-chr11:65411627..65413342,3	MCF-7	breast:
6	chr11:65411140..65413150-chr11:65624736..65627560,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4489	TF binding region
SIPA1	TF binding region
ENSG00000172732	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000162300	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10896027	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11227248	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11227249	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11227250	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11227261	0.83[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1205259	0.90[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs12281400	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1784223	0.90[MEX][hapmap];0.80[EUR][1000 genomes]
rs1787034	0.90[MEX][hapmap]
rs2509948	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs3372	0.86[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs34007146	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34462081	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930156	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930304	1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs573589	0.86[MEX][hapmap]
rs7395672	0.82[MEX][hapmap]
rs7944860	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
4	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
5	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
6	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS 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 miRNA target site	102 gene(s)	inside rSNPs	diseases
8	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
9	nsv468599	chr11:65335705-65427346	ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv555213	chr11:65335705-65427346	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
11	nsv897732	chr11:65335705-65427346	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS 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 miRNA target site	78 gene(s)	inside rSNPs	diseases
12	nsv468600	chr11:65335705-65431360	Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv555214	chr11:65335705-65431360	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
14	nsv897733	chr11:65335705-65431360	Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
15	nsv897734	chr11:65335705-65436888	Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
16	nsv897735	chr11:65335705-65481166	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
17	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
18	nsv897746	chr11:65349756-65427346	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
19	nsv897747	chr11:65353906-65481166	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
20	esv1831135	chr11:65387352-65420872	Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	43 gene(s)	inside rSNPs	diseases
21	nsv897748	chr11:65392695-65466911	Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
22	nsv897749	chr11:65401748-65420760	Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	39 gene(s)	inside rSNPs	diseases
23	nsv897750	chr11:65401748-65421476	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
24	nsv897751	chr11:65401748-65425167	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
25	nsv897752	chr11:65405300-65421476	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
26	nsv897753	chr11:65405300-65422693	Genic enhancers Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
27	nsv897754	chr11:65405300-65436888	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
28	nsv897755	chr11:65405300-65481166	Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
29	nsv897756	chr11:65406393-65425167	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
30	nsv897757	chr11:65406393-65427568	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2448490	SNX32	cis	cerebellum	SCAN
rs2448490	ZBTB3	cis	parietal	SCAN
rs2448490	RNASEH2C	cis	parietal	SCAN
rs2448490	SLC22A10	cis	parietal	SCAN
rs2448490	SIPA1	cis	cerebellum	SCAN
rs2448490	SNX32	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65406400-65413000	Weak transcription	Fetal Heart	heart
2	chr11:65406400-65414600	Weak transcription	Ovary	ovary
3	chr11:65406400-65416800	Weak transcription	Aorta	Aorta
4	chr11:65406600-65412800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:65406600-65412800	Weak transcription	HSMMtube	muscle
6	chr11:65406600-65414400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:65406600-65414400	Weak transcription	NHEK	skin
8	chr11:65406600-65414600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:65406600-65414600	Weak transcription	Osteobl	bone
10	chr11:65406600-65419200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:65407000-65415000	Genic enhancers	Fetal Muscle Trunk	muscle
12	chr11:65407800-65413000	Weak transcription	NHDF-Ad	bronchial
13	chr11:65408800-65414800	Genic enhancers	Spleen	Spleen
14	chr11:65409000-65414200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:65409200-65412600	Weak transcription	Dnd41	blood
16	chr11:65409200-65416200	Weak transcription	Fetal Lung	lung
17	chr11:65409200-65419000	Weak transcription	Right Atrium	heart
18	chr11:65409400-65412400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr11:65409400-65412600	Weak transcription	Liver	Liver
20	chr11:65409400-65412800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:65409400-65414400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:65409400-65415000	Weak transcription	Brain Angular Gyrus	brain
23	chr11:65409600-65412200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr11:65409600-65412200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:65409600-65412200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:65409600-65412200	Weak transcription	Left Ventricle	heart
27	chr11:65409600-65412400	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr11:65409600-65412600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr11:65409600-65412600	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:65409600-65413000	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr11:65409600-65413400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr11:65409600-65414400	Weak transcription	Brain Substantia Nigra	brain
33	chr11:65409600-65414400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:65409600-65414400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:65409600-65415200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:65409600-65416000	Strong transcription	Thymus	Thymus
37	chr11:65410000-65412200	Weak transcription	Brain Anterior Caudate	brain
38	chr11:65410000-65412400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:65410000-65412400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:65410000-65413400	Weak transcription	Brain Hippocampus Middle	brain
41	chr11:65410000-65413400	Strong transcription	Fetal Stomach	stomach
42	chr11:65410000-65414000	Strong transcription	Right Ventricle	heart
43	chr11:65410000-65414400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:65410000-65414400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr11:65410000-65414400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:65410000-65414400	Weak transcription	Stomach Mucosa	stomach
47	chr11:65410000-65414600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:65410000-65416400	Strong transcription	Adipose Nuclei	Adipose
49	chr11:65410000-65417000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:65410200-65412200	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links