Variant report

Variant	rs7925824
Chromosome Location	chr11:45929961-45929962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:45927639-45933214	K562	blood:	n/a	n/a
2	PBX3	chr11:45929141-45929999	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr11:45929927-45930824	GM12891	blood:	n/a	n/a
4	POLR2A	chr11:45928491-45930580	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:45929461-45930151	U87	brain:	n/a	n/a
6	POLR2A	chr11:45929664-45930741	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr11:45927836-45930385	IMR90	lung:	n/a	n/a
8	POLR2A	chr11:45928064-45933219	GM12878	blood:	n/a	n/a
9	PML	chr11:45929722-45930171	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:45928768-45931201	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr11:45928619-45930952	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr11:45929240-45930463	U87	brain:	n/a	n/a
13	POLR2A	chr11:45929432-45930871	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr11:45927693-45931524	GM19193	blood:	n/a	n/a
15	POLR2A	chr11:45924858-45931217	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr11:45927964-45931067	K562	blood:	n/a	n/a
17	POLR2A	chr11:45929702-45931202	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:45929569-45930332	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr11:45927669-45931028	GM12891	blood:	n/a	n/a
20	POLR2A	chr11:45929234-45930520	U87	brain:	n/a	n/a
21	POLR2A	chr11:45928685-45931048	HL-60	blood:	n/a	n/a
22	POLR2A	chr11:45929502-45930881	NB4	blood:	n/a	n/a
23	POLR2A	chr11:45929268-45930885	GM15510	blood:	n/a	n/a
24	POLR2A	chr11:45927698-45930572	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr11:45927964-45931104	H1-neurons	neurons:	n/a	n/a
26	NFATC1	chr11:45929422-45930056	GM12878	blood:	n/a	n/a
27	POLR2A	chr11:45929243-45930953	HepG2	liver:	n/a	n/a
28	POLR2A	chr11:45929611-45930793	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr11:45927664-45931204	K562	blood:	n/a	n/a
30	POLR2A	chr11:45927817-45930803	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr11:45927779-45931204	PBDE	blood:	n/a	n/a
32	POLR2A	chr11:45927562-45931241	GM12891	blood:	n/a	n/a
33	POLR2A	chr11:45927421-45931267	GM12892	blood:	n/a	n/a
34	POLR2A	chr11:45927707-45931335	GM12878	blood:	n/a	n/a
35	POLR2A	chr11:45927764-45931022	GM18951	blood:	n/a	n/a
36	POLR2A	chr11:45929921-45930154	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr11:45929223-45931126	GM12892	blood:	n/a	n/a
38	POLR2A	chr11:45927753-45932920	GM18505	blood:	n/a	n/a
39	POLR2A	chr11:45927831-45930459	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr11:45929713-45930343	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr11:45929901-45930144	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr11:45927501-45931242	K562	blood:	n/a	n/a
43	POLR2A	chr11:45928206-45931597	GM12891	blood:	n/a	n/a
44	NFATC1	chr11:45929959-45930278	GM12878	blood:	n/a	n/a
45	POLR2A	chr11:45927292-45932078	GM12892	blood:	n/a	n/a
46	POLR2A	chr11:45929796-45930272	A549	lung:	n/a	n/a
47	POLR2A	chr11:45928390-45930058	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr11:45928698-45930553	PANC-1	pancreas:	n/a	n/a
49	ELF1	chr11:45929772-45930273	GM12878	blood:	n/a	n/a
50	POLR2A	chr11:45929126-45931354	HL-60	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45928634..45930948-chr12:122237013..122238884,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255498	TF binding region
C11orf94	TF binding region
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10838530	0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs10838531	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10838563	1.00[CEU][hapmap]
rs11038706	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1132349	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11600112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271847	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280331	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3802758	0.86[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7109981	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7115790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7124323	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7124434	0.82[ASN][1000 genomes]
rs867813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs939108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1047462	chr11:45898630-45953696	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1794798	chr11:45903280-45953636	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv1805505	chr11:45912324-45956109	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv1807609	chr11:45915859-45940195	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv1798496	chr11:45925495-45948304	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45921400-45933000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:45921600-45931400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr11:45922200-45931800	Weak transcription	Primary B cells from cord blood	blood
4	chr11:45922400-45934800	Weak transcription	A549	lung
5	chr11:45922600-45930600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:45922600-45930800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:45922600-45931400	Weak transcription	Aorta	Aorta
8	chr11:45922600-45932400	Weak transcription	Hela-S3	cervix
9	chr11:45922600-45932400	Weak transcription	Osteobl	bone
10	chr11:45922600-45934400	Weak transcription	HMEC	breast
11	chr11:45922600-45938400	Weak transcription	Fetal Kidney	kidney
12	chr11:45922800-45930000	Weak transcription	Left Ventricle	heart
13	chr11:45922800-45930400	Weak transcription	Liver	Liver
14	chr11:45923000-45930600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:45923000-45938000	Weak transcription	NHDF-Ad	bronchial
16	chr11:45923000-45938400	Weak transcription	Right Atrium	heart
17	chr11:45923200-45931200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:45923200-45932200	Weak transcription	HSMM	muscle
19	chr11:45923200-45935600	Weak transcription	NH-A	brain
20	chr11:45923400-45931600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:45923400-45932000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:45923400-45932400	Weak transcription	HepG2	liver
23	chr11:45923400-45934800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:45923600-45936600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:45924400-45930400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:45924600-45936400	Strong transcription	Fetal Brain Female	brain
27	chr11:45925600-45930600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr11:45925800-45930400	Weak transcription	Fetal Intestine Large	intestine
29	chr11:45925800-45931200	Weak transcription	Primary T cells from cord blood	blood
30	chr11:45926200-45931000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:45926200-45931200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:45926200-45931200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:45926200-45931200	Weak transcription	Fetal Thymus	thymus
34	chr11:45926200-45931400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr11:45926400-45930600	Weak transcription	Lung	lung
36	chr11:45926400-45930600	Weak transcription	NHLF	lung
37	chr11:45926400-45931000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:45926600-45935400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:45926800-45930600	Enhancers	Pancreas	Pancrea
40	chr11:45927000-45930800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:45927000-45930800	Weak transcription	Adipose Nuclei	Adipose
42	chr11:45927000-45931200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr11:45927000-45931200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:45927000-45932200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:45927000-45936200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr11:45927000-45936600	Weak transcription	K562	blood
47	chr11:45927200-45931200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr11:45927200-45931400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:45927200-45937600	Weak transcription	Stomach Mucosa	stomach
50	chr11:45927400-45930200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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