Variant report

Variant	rs12576169
Chromosome Location	chr11:65405059-65405060
allele	C/G
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	chr11:65404967-65405086	K562	blood:	n/a	n/a
2	POLR2A	chr11:65404916-65406624	PFSK-1	brain:	n/a	n/a
3	NR2F2	chr11:65404983-65406269	K562	blood:	n/a	n/a
4	MAX	chr11:65404960-65406338	K562	blood:	n/a	chr11:65406147-65406157
5	NR2F2	chr11:65403273-65406510	K562	blood:	n/a	n/a
6	MTA3	chr11:65404986-65405593	GM12878	blood:	n/a	n/a
7	MXI1	chr11:65404961-65406714	IMR90	lung:	n/a	n/a
8	POLR2A	chr11:65405019-65406689	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr11:65404961-65406188	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr11:65405039-65406323	A549	lung:	n/a	chr11:65405916-65405925 chr11:65405910-65405928 chr11:65405339-65405352 chr11:65406055-65406065 chr11:65405341-65405349
11	POLR2A	chr11:65405014-65406521	PANC-1	pancreas:	n/a	n/a
12	CTCF	chr11:65404928-65405822	SK-N-SH	brain:	n/a	chr11:65405339-65405352 chr11:65405341-65405349
13	MAX	chr11:65405030-65406478	A549	lung:	n/a	chr11:65406393-65406403 chr11:65406147-65406157
14	POLR2A	chr11:65404913-65405264	GM12891	blood:	n/a	n/a
15	PML	chr11:65405032-65406695	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:65404968-65406369	HepG2	liver:	n/a	n/a
17	POLR2A	chr11:65404870-65410346	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:65405042-65406670	PFSK-1	brain:	n/a	n/a
19	HCFC1	chr11:65404897-65406682	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr11:65405002-65406700	GM12892	blood:	n/a	n/a
21	TCF12	chr11:65405046-65406405	A549	lung:	n/a	chr11:65405472-65405480
22	POLR2A	chr11:65405031-65406574	SK-N-MC	brain:	n/a	n/a
23	ESRRA	chr11:65404865-65408545	GM12878	blood:	n/a	chr11:65407590-65407609 chr11:65405025-65405043 chr11:65407594-65407607 chr11:65407590-65407604 chr11:65407860-65407873 chr11:65407733-65407746
24	MAZ	chr11:65405011-65406567	IMR90	lung:	n/a	chr11:65406393-65406403 chr11:65406147-65406157
25	POLR2A	chr11:65404988-65406673	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65380696..65385200-chr11:65403578..65408941,10	MCF-7	breast:
2	chr11:65265497..65267860-chr11:65403489..65405848,3	K562	blood:
3	chr11:65403669..65406096-chr11:65480097..65481780,2	MCF-7	breast:
4	chr11:65324365..65326095-chr11:65402996..65405366,2	K562	blood:
5	chr11:65342220..65345077-chr11:65403229..65406787,3	K562	blood:
6	chr11:65401684..65407000-chr11:65623220..65627704,6	K562	blood:
7	chr11:65404733..65406830-chr11:65478478..65481431,2	K562	blood:
8	chr11:65336849..65339116-chr11:65404161..65406035,2	K562	blood:

Variant related genes	Relation type
SIPA1	TF binding region
ENSG00000172977	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000197136	Chromatin interaction
ENSG00000173442	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11227240	0.89[ASN][1000 genomes]
rs11227253	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11227264	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11227265	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11227267	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11227269	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1144788	0.93[ASN][1000 genomes]
rs12575137	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4645926	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65398000-65405200	Genic enhancers	Spleen	Spleen
2	chr11:65400800-65406600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:65401400-65405200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:65402000-65405200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:65403000-65405600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:65403600-65405200	Genic enhancers	Liver	Liver
7	chr11:65403800-65405200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr11:65403800-65405400	Genic enhancers	Placenta	Placenta
9	chr11:65404200-65405200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:65404200-65405200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:65404200-65405200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
12	chr11:65404400-65405200	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr11:65404400-65405200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:65404400-65405200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:65404400-65405200	Enhancers	Fetal Heart	heart
16	chr11:65404400-65405200	Genic enhancers	Fetal Stomach	stomach
17	chr11:65404400-65405200	Genic enhancers	HSMM	muscle
18	chr11:65404400-65405200	Genic enhancers	NHDF-Ad	bronchial
19	chr11:65404400-65405400	Enhancers	Right Atrium	heart
20	chr11:65404400-65405400	Flanking Active TSS	Hela-S3	cervix
21	chr11:65404400-65405400	Enhancers	HMEC	breast
22	chr11:65404600-65405200	Enhancers	Primary hematopoietic stem cells	blood
23	chr11:65404600-65405200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:65404600-65405200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:65404600-65405200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:65404600-65405200	Genic enhancers	Brain Hippocampus Middle	brain
27	chr11:65404600-65405200	Genic enhancers	Brain Substantia Nigra	brain
28	chr11:65404600-65405200	Genic enhancers	Fetal Intestine Large	intestine
29	chr11:65404600-65405200	Genic enhancers	Fetal Thymus	thymus
30	chr11:65404600-65405200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:65404600-65405200	Enhancers	Right Ventricle	heart
32	chr11:65404600-65405400	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr11:65404600-65405600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:65404600-65405600	Weak transcription	Ovary	ovary
35	chr11:65404600-65405600	Enhancers	Stomach Mucosa	stomach
36	chr11:65404600-65405600	Enhancers	HUVEC	blood vessel
37	chr11:65404800-65405200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:65404800-65405200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:65404800-65405200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:65404800-65405200	Weak transcription	Aorta	Aorta
41	chr11:65404800-65405200	Enhancers	Fetal Kidney	kidney
42	chr11:65404800-65405200	Enhancers	Left Ventricle	heart
43	chr11:65404800-65405200	Weak transcription	Lung	lung
44	chr11:65404800-65405200	Genic enhancers	Rectal Smooth Muscle	rectum
45	chr11:65404800-65405200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
46	chr11:65404800-65405400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr11:65404800-65405400	Flanking Active TSS	HepG2	liver
48	chr11:65404800-65405600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:65404800-65405600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:65404800-65405600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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