Variant report

Variant	rs12790427
Chromosome Location	chr11:65384727-65384728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65384641-65385203	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:65380316-65385264	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:65384655-65384841	K562	blood:	n/a	n/a
4	CTCF	chr11:65384700-65384850	GM12875	blood:	n/a	n/a
5	POLR2A	chr11:65380283-65385739	GM12878	blood:	n/a	n/a
6	CTCF	chr11:65384720-65384870	Caco-2	colon:	n/a	n/a
7	POLR2A	chr11:65383885-65385237	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr11:65384655-65384916	GM12878	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65382643..65384929-chr11:65635582..65638350,2	K562	blood:
2	chr11:65263855..65269766-chr11:65381384..65386650,8	MCF-7	breast:
3	chr11:65384023..65385881-chr11:65486262..65488402,2	MCF-7	breast:
4	chr11:65383055..65385315-chr11:65656769..65659288,2	K562	blood:
5	chr11:65384276..65386972-chr11:65478689..65481320,2	K562	blood:
6	chr11:65380932..65386957-chr11:65428679..65431812,7	MCF-7	breast:
7	chr11:65380696..65385200-chr11:65403578..65408941,10	MCF-7	breast:
8	chr11:65381837..65384874-chr11:65408944..65413829,9	MCF-7	breast:
9	chr11:65336061..65346997-chr11:65371025..65390625,42	MCF-7	breast:
10	chr11:65187686..65190825-chr11:65382299..65384886,3	K562	blood:
11	chr11:65383395..65385868-chr11:65617550..65620043,2	MCF-7	breast:
12	chr11:65335401..65344755-chr11:65379602..65385163,20	K562	blood:
13	chr11:65265142..65268654-chr11:65382786..65385771,3	K562	blood:
14	chr11:65381571..65386287-chr11:65427993..65433260,8	MCF-7	breast:
15	chr11:65317777..65320540-chr11:65382585..65385188,2	K562	blood:
16	chr11:65383137..65385926-chr11:65685879..65687522,2	MCF-7	breast:
17	chr11:65379754..65386537-chr11:65415130..65425067,26	MCF-7	breast:
18	chr11:65382961..65385315-chr11:65657365..65660183,3	K562	blood:
19	chr11:65309008..65312326-chr11:65383111..65384790,3	K562	blood:
20	chr11:65264270..65268654-chr11:65380562..65385771,6	K562	blood:
21	chr11:65189868..65193892-chr11:65380372..65385774,5	MCF-7	breast:

No data

Variant related genes	Relation type
PCNXL3	TF binding region
MAP3K11	TF binding region
ENSG00000173442	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000266041	Chromatin interaction
ENSG00000172638	Chromatin interaction
ENSG00000172922	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000265874	Chromatin interaction
ENSG00000173465	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000176973	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000260233	Chromatin interaction
ENSG00000213445	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1078457	0.97[EUR][1000 genomes]
rs12801636	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4930295	0.81[EUR][1000 genomes]
rs66864335	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
5	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
6	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv897739	chr11:65337714-65388300	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
21	esv2761680	chr11:65344328-65391317	Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	46 gene(s)	inside rSNPs	diseases
22	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
23	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65383600-65384800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:65383800-65384800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr11:65383800-65384800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr11:65383800-65384800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:65383800-65384800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:65383800-65384800	Flanking Active TSS	Rectal Smooth Muscle	rectum
7	chr11:65383800-65384800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr11:65383800-65387400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:65384000-65384800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:65384000-65384800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:65384000-65384800	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
12	chr11:65384000-65384800	Flanking Active TSS	Fetal Lung	lung
13	chr11:65384000-65384800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
14	chr11:65384000-65384800	Flanking Active TSS	HMEC	breast
15	chr11:65384000-65385000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
16	chr11:65384000-65385600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:65384200-65384800	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr11:65384200-65384800	Weak transcription	Aorta	Aorta
19	chr11:65384200-65384800	Enhancers	Fetal Heart	heart
20	chr11:65384200-65384800	Flanking Active TSS	Fetal Intestine Large	intestine
21	chr11:65384200-65384800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
22	chr11:65384200-65384800	Enhancers	Stomach Mucosa	stomach
23	chr11:65384200-65385000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:65384200-65385000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
25	chr11:65384200-65385000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
26	chr11:65384200-65385000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
27	chr11:65384200-65385000	Enhancers	Fetal Brain Male	brain
28	chr11:65384200-65385000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
29	chr11:65384200-65385000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
30	chr11:65384200-65385000	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr11:65384200-65385000	Transcr. at gene 5' and 3'	K562	blood
32	chr11:65384200-65385200	Transcr. at gene 5' and 3'	A549	lung
33	chr11:65384200-65385200	Transcr. at gene 5' and 3'	NHLF	lung
34	chr11:65384200-65385400	Flanking Active TSS	GM12878-XiMat	blood
35	chr11:65384200-65385600	Genic enhancers	Spleen	Spleen
36	chr11:65384200-65385600	Transcr. at gene 5' and 3'	Hela-S3	cervix
37	chr11:65384200-65385800	Weak transcription	Small Intestine	intestine
38	chr11:65384200-65389600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:65384400-65384800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr11:65384400-65384800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:65384400-65384800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr11:65384400-65384800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:65384400-65384800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
44	chr11:65384400-65384800	Weak transcription	Ovary	ovary
45	chr11:65384400-65384800	Enhancers	Right Atrium	heart
46	chr11:65384400-65385000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:65384400-65385000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:65384400-65385000	Enhancers	Primary B cells from peripheral blood	blood
49	chr11:65384400-65385000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr11:65384400-65385000	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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