Variant report

Variant	rs2241304
Chromosome Location	chr11:65819014-65819015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr11:65818427-65820727	H1-neurons	neurons:	n/a	chr11:65819271-65819284
2	POLR2A	chr11:65818957-65820651	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr11:65818920-65820451	SK-N-MC	brain:	n/a	n/a
4	SREBP1	chr11:65818393-65820311	GM12878	blood:	n/a	n/a
5	JUN	chr11:65818036-65820665	K562	blood:	n/a	n/a
6	POLR2A	chr11:65818350-65820369	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:65818922-65820351	PFSK-1	brain:	n/a	n/a
8	SIN3AK20	chr11:65818999-65820473	MCF-7	breast:	n/a	n/a
9	TCF12	chr11:65818989-65820221	ECC-1	luminal epithelium:	n/a	chr11:65819268-65819278
10	TAF1	chr11:65818986-65820309	ECC-1	luminal epithelium:	n/a	n/a
11	HCFC1	chr11:65818081-65820872	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:65818724-65820538	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr11:65818835-65820316	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:65818898-65820298	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr11:65818987-65820115	HCT-116	colon:	n/a	n/a
16	ELF1	chr11:65818958-65820340	HCT-116	colon:	n/a	chr11:65819601-65819613 chr11:65819556-65819568 chr11:65819819-65819830 chr11:65819571-65819580 chr11:65819819-65819830 chr11:65819820-65819829 chr11:65819818-65819831 chr11:65819315-65819327
17	POLR2A	chr11:65818396-65820171	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr11:65818975-65820418	GM12892	blood:	n/a	n/a
19	SIN3AK20	chr11:65818889-65820728	MCF-7	breast:	n/a	n/a
20	PML	chr11:65819013-65820378	GM12878	blood:	n/a	n/a
21	MAZ	chr11:65818871-65820883	IMR90	lung:	n/a	chr11:65819555-65819565
22	TCF12	chr11:65818899-65820631	A549	lung:	n/a	chr11:65818899-65818906 chr11:65819268-65819278
23	MTA3	chr11:65818342-65820298	GM12878	blood:	n/a	n/a
24	GABPA	chr11:65818937-65820634	MCF-7	breast:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65816864..65823380-chr11:65832037..65840391,16	MCF-7	breast:
2	chr11:65778958..65780961-chr11:65818944..65820828,4	MCF-7	breast:
3	chr11:65599682..65601863-chr11:65818746..65820444,2	K562	blood:
4	chr11:65812475..65816551-chr11:65816982..65820716,11	MCF-7	breast:
5	chr11:65767679..65771369-chr11:65818165..65822112,6	MCF-7	breast:
6	chr11:65766270..65769793-chr11:65817988..65822487,7	MCF-7	breast:
7	chr11:65788326..65791572-chr11:65817870..65821514,6	MCF-7	breast:
8	chr11:65624197..65629461-chr11:65817994..65821738,6	K562	blood:
9	chr11:65727969..65730897-chr11:65818847..65821349,3	MCF-7	breast:
10	chr11:65666594..65669601-chr11:65818513..65821111,3	K562	blood:
11	chr11:65768250..65771590-chr11:65817294..65821421,6	K562	blood:
12	chr11:65624171..65627161-chr11:65818449..65820914,2	K562	blood:
13	chr11:65686637..65688948-chr11:65818033..65819758,2	MCF-7	breast:
14	chr11:65654406..65656554-chr11:65818022..65819720,2	MCF-7	breast:
15	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:
16	chr11:65429132..65431872-chr11:65817636..65822281,4	MCF-7	breast:
17	chr11:65818576..65820605-chr11:66044652..66046444,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SF3B2-1	chr11:65818991-65819074	NONHSAT022260
2	lnc-GAL3ST3-1	chr11:65818545-65820124	ncRnaDb_ncrna_FR023308_1

No data

Variant related genes	Relation type
SF3B2	TF binding region
GAL3ST3	TF binding region
ENSG00000238752	TF binding region
ENSG00000175115	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000172803	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000254452	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000245156	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000174871	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175315	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10896065	1.00[JPT][hapmap]
rs11227393	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11227396	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12099359	1.00[JPT][hapmap]
rs12574568	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12575735	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12576319	1.00[JPT][hapmap]
rs2276015	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs28372938	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3825068	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4930169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs653955	1.00[JPT][hapmap]
rs7940700	1.00[JPT][hapmap]
rs9326362	1.00[JPT][hapmap]

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	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65814200-65819200	Enhancers	Pancreas	Pancrea
2	chr11:65818200-65819200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:65818200-65819200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr11:65818200-65819200	Enhancers	Spleen	Spleen
5	chr11:65818200-65819200	Flanking Active TSS	HepG2	liver
6	chr11:65818200-65819800	Enhancers	Stomach Mucosa	stomach
7	chr11:65818400-65819200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:65818400-65819200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr11:65818400-65819200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr11:65818400-65819200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:65818400-65819200	Flanking Active TSS	Dnd41	blood
12	chr11:65818400-65819200	Flanking Active TSS	Hela-S3	cervix
13	chr11:65818600-65819200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:65818600-65819200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:65818600-65819200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:65818600-65819200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:65818600-65819200	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr11:65818600-65819200	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr11:65818600-65819200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr11:65818600-65819200	Flanking Active TSS	Fetal Brain Male	brain
21	chr11:65818600-65819200	Flanking Active TSS	Fetal Heart	heart
22	chr11:65818600-65819200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr11:65818600-65819200	Flanking Active TSS	A549	lung
24	chr11:65818600-65819400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr11:65818600-65819400	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr11:65818600-65819400	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr11:65818600-65819400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr11:65818600-65819400	Flanking Active TSS	GM12878-XiMat	blood
29	chr11:65818600-65819600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:65818600-65819600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:65818600-65819600	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr11:65818800-65819200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
33	chr11:65818800-65819200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:65818800-65819200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr11:65818800-65819200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:65818800-65819200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr11:65818800-65819200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:65818800-65819200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr11:65818800-65819200	Flanking Active TSS	Brain Cingulate Gyrus	brain
40	chr11:65818800-65819200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr11:65818800-65819200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
42	chr11:65818800-65819200	Flanking Active TSS	Fetal Kidney	kidney
43	chr11:65818800-65819200	Flanking Active TSS	Fetal Lung	lung
44	chr11:65818800-65819200	Enhancers	Lung	lung
45	chr11:65818800-65819200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr11:65818800-65819200	Enhancers	Small Intestine	intestine
47	chr11:65818800-65819200	Flanking Active TSS	Thymus	Thymus
48	chr11:65818800-65819200	Flanking Active TSS	HSMM	muscle
49	chr11:65818800-65819400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr11:65818800-65819400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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