Variant report

Variant	rs11038341
Chromosome Location	chr11:45203212-45203213
allele	C/T
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	POLR2A	chr11:45201038-45203556	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr11:45201832-45203358	HepG2	liver:	n/a	n/a
3	ZBTB7A	chr11:45201489-45203332	ECC-1	luminal epithelium:	n/a	chr11:45202789-45202798
4	HCFC1	chr11:45200158-45203524	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr11:45201810-45203261	HepG2	liver:	n/a	n/a
6	MAX	chr11:45201651-45203217	HepG2	liver:	n/a	chr11:45202435-45202445 chr11:45202681-45202691 chr11:45201752-45201762
7	SMARCB1	chr11:45201442-45203625	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr11:45200459-45203366	IMR90	lung:	n/a	chr11:45202435-45202445 chr11:45202681-45202691 chr11:45201752-45201762
9	SMARCC1	chr11:45202438-45203572	Hela-S3	cervix:	n/a	n/a
10	HNF4A	chr11:45202809-45203242	HepG2	liver:	n/a	chr11:45202996-45203008 chr11:45202996-45203008 chr11:45202993-45203011 chr11:45203001-45203016 chr11:45203000-45203018 chr11:45202991-45203013 chr11:45202995-45203009 chr11:45202995-45203008 chr11:45203002-45203015 chr11:45203003-45203015 chr11:45202994-45203009 chr11:45203003-45203015 chr11:45202996-45203009 chr11:45202995-45203009 chr11:45202996-45203008
11	TFAP2A	chr11:45201279-45203316	Hela-S3	cervix:	n/a	chr11:45201846-45201856 chr11:45202003-45202018 chr11:45202609-45202623 chr11:45202165-45202177 chr11:45201844-45201858 chr11:45202004-45202012 chr11:45202790-45202802 chr11:45201846-45201856 chr11:45202611-45202621 chr11:45202165-45202177 chr11:45202611-45202621 chr11:45202611-45202621 chr11:45201846-45201861 chr11:45202001-45202013 chr11:45202165-45202177 chr11:45201844-45201858 chr11:45202611-45202626 chr11:45202611-45202621 chr11:45202411-45202423 chr11:45202004-45202012 chr11:45201844-45201856 chr11:45202004-45202012 chr11:45202165-45202177 chr11:45202791-45202802 chr11:45201846-45201856

No.	Distal block	Cell Line	Cell type
1	chr11:45192972..45194599-chr11:45201172..45203381,2	MCF-7	breast:
2	chr11:45197003..45199885-chr11:45200062..45203295,4	MCF-7	breast:
3	chr11:45164160..45171283-chr11:45198764..45207868,26	MCF-7	breast:
4	chr11:45167893..45171206-chr11:45200303..45204446,5	MCF-7	breast:
5	chr11:45167440..45169930-chr11:45202656..45204248,2	K562	blood:
6	chr11:45201511..45203799-chr11:45256779..45259525,2	MCF-7	breast:

Variant related genes	Relation type
PRDM11	TF binding region
ENSG00000254664	Chromatin interaction
ENSG00000019485	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10444286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769123	0.82[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838428	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838439	0.82[JPT][hapmap]
rs11038339	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11038350	0.85[JPT][hapmap];0.88[AMR][1000 genomes]
rs11038357	1.00[CHB][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs11601021	0.83[MEX][hapmap]
rs12284404	0.83[AMR][1000 genomes]
rs12292233	1.00[YRI][hapmap]
rs17723470	1.00[CHB][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs3758723	1.00[CHB][hapmap];0.83[TSI][hapmap]
rs3886790	0.89[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55646648	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72907072	0.92[ASN][1000 genomes]
rs7940871	1.00[CHB][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	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	esv3406728	chr11:45201001-45203549	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3326620	chr11:45201401-45203949	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11038341	ACP2	cis	parietal	SCAN
rs11038341	SLC38A6	trans	cerebellum	SCAN
rs11038341	PRDM11	cis	Thyroid	GTEx
rs11038341	SYT13	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45201400-45203400	Flanking Active TSS	Colonic Mucosa	Colon
2	chr11:45201400-45203400	Enhancers	Fetal Brain Male	brain
3	chr11:45201600-45203600	Active TSS	Aorta	Aorta
4	chr11:45201800-45204000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:45202000-45204600	Weak transcription	Liver	Liver
6	chr11:45202000-45205400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:45202000-45206600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:45202000-45207600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:45202000-45220000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:45202200-45204600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:45202400-45203400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:45202400-45203400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:45202400-45203600	Enhancers	Stomach Mucosa	stomach
14	chr11:45202400-45204200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:45202600-45203400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:45202600-45203400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr11:45202600-45203400	Flanking Active TSS	Pancreas	Pancrea
18	chr11:45202600-45203400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr11:45202600-45203400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr11:45202600-45203400	Flanking Active TSS	HUVEC	blood vessel
21	chr11:45202600-45203600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr11:45202600-45203600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:45202600-45203600	Flanking Active TSS	Fetal Lung	lung
24	chr11:45202600-45203600	Flanking Active TSS	Fetal Muscle Trunk	muscle
25	chr11:45202600-45203600	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr11:45202600-45203800	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr11:45202600-45204000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr11:45202600-45204600	Weak transcription	Primary B cells from cord blood	blood
29	chr11:45202800-45203400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:45202800-45203400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr11:45202800-45203400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:45202800-45203400	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr11:45202800-45203400	Flanking Active TSS	Fetal Heart	heart
34	chr11:45202800-45203400	Enhancers	Placenta	Placenta
35	chr11:45202800-45203400	Flanking Active TSS	A549	lung
36	chr11:45202800-45203600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr11:45202800-45203600	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr11:45202800-45203600	Flanking Active TSS	Left Ventricle	heart
39	chr11:45202800-45203800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr11:45202800-45203800	Flanking Active TSS	Right Ventricle	heart
41	chr11:45202800-45204000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:45202800-45204000	Flanking Active TSS	Hela-S3	cervix
43	chr11:45202800-45206200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr11:45202800-45234000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:45203000-45203400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
46	chr11:45203000-45203400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:45203000-45203400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
48	chr11:45203000-45203400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:45203000-45203400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr11:45203000-45203400	Enhancers	Cortex derived primary cultured neurospheres	brain

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