Variant report

Variant	rs12269752
Chromosome Location	chr11:18431249-18431250
allele	A/G
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:13)
LncRNA
region (count:0)
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	POLR2A	chr11:18431072-18431314	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:18428875-18431440	A549	lung:	n/a	n/a
3	POLR2A	chr11:18429472-18431508	IMR90	lung:	n/a	n/a
4	POLR2A	chr11:18428498-18431298	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr11:18429487-18431430	ProgFib	skin:	n/a	n/a
6	POLR2A	chr11:18415270-18432749	U87	brain:	n/a	n/a
7	POLR2A	chr11:18431166-18431396	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:18426347-18431429	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr11:18428177-18432634	U87	brain:	n/a	n/a
10	POLR2A	chr11:18428440-18431439	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:18428593-18431268	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:18431210-18431371	MCF-7	breast:	n/a	n/a
13	POLR2A	chr11:18428444-18431399	K562	blood:	n/a	n/a
14	POLR2A	chr11:18429611-18431310	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr11:18428323-18432585	GM12878	blood:	n/a	n/a
16	POLR2A	chr11:18431068-18432523	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr11:18429466-18431465	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr11:18428613-18431437	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:18431130-18431399	K562	blood:	n/a	n/a
20	POLR2A	chr11:18415373-18432749	U87	brain:	n/a	n/a
21	POLR2A	chr11:18429384-18431438	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr11:18431062-18431386	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:18428609-18431544	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr11:18431198-18431422	HCT-116	colon:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18430457..18432481-chr11:18456231..18458824,2	K562	blood:
2	chr11:18415543..18417980-chr11:18429058..18431461,3	K562	blood:
3	chr11:18428578..18433796-chr11:18433952..18441799,12	K562	blood:
4	chr11:18429708..18432011-chr11:18438993..18440849,2	MCF-7	breast:
5	chr11:18429091..18432597-chr11:18437736..18442022,5	K562	blood:
6	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:
7	chr11:18338559..18340815-chr11:18429973..18431538,2	K562	blood:
8	chr11:18430992..18433594-chr11:18671547..18674322,2	K562	blood:
9	chr11:18429496..18431588-chr11:18458511..18461417,2	K562	blood:
10	chr11:18415873..18420206-chr11:18430045..18435036,6	MCF-7	breast:
11	chr11:18429142..18431296-chr11:18432609..18435165,2	K562	blood:
12	chr11:18423297..18429050-chr11:18429237..18433863,11	K562	blood:
13	chr11:18430626..18432747-chr11:18545645..18547445,2	K562	blood:

No data

Variant related genes	Relation type
LDHC	TF binding region
ENSG00000256006	Chromatin interaction
ENSG00000166796	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10832925	0.93[EUR][1000 genomes]
rs10832928	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11024637	0.97[EUR][1000 genomes]
rs11024642	1.00[EUR][1000 genomes]
rs11024644	1.00[EUR][1000 genomes]
rs12273776	0.93[EUR][1000 genomes]
rs12274166	0.93[EUR][1000 genomes]
rs12274651	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12275692	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12276166	0.93[EUR][1000 genomes]
rs12284013	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12284667	0.93[EUR][1000 genomes]
rs12287183	0.93[EUR][1000 genomes]
rs12801224	0.83[AMR][1000 genomes]
rs12804008	1.00[EUR][1000 genomes]
rs34546419	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs36043375	0.83[AMR][1000 genomes]
rs7932887	1.00[CEU][hapmap];1.00[EUR][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	esv1811183	chr11:18389643-18432437	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers 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	56 gene(s)	inside rSNPs	diseases
7	nsv982991	chr11:18424852-18431306	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 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	chr11:18418200-18433800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18418400-18433200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:18419000-18431400	Strong transcription	HSMM	muscle
4	chr11:18422000-18433800	Weak transcription	Stomach Mucosa	stomach
5	chr11:18422200-18433800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:18422600-18433800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:18426400-18433800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:18427200-18433800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:18427200-18433800	Weak transcription	Fetal Heart	heart
10	chr11:18427200-18433800	Weak transcription	Small Intestine	intestine
11	chr11:18427400-18433400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:18428000-18432600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:18428000-18433600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:18428000-18433800	Weak transcription	Colonic Mucosa	Colon
15	chr11:18428000-18433800	Weak transcription	Gastric	stomach
16	chr11:18428200-18433600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:18429000-18433600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:18429200-18433400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:18429200-18433600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:18429200-18433800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr11:18429400-18432200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr11:18429600-18434200	Weak transcription	HepG2	liver
23	chr11:18429800-18431400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:18429800-18431400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:18429800-18433400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:18429800-18433400	Weak transcription	Fetal Kidney	kidney
27	chr11:18430000-18431600	Weak transcription	Hela-S3	cervix
28	chr11:18430000-18432200	Weak transcription	Dnd41	blood
29	chr11:18430000-18433800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr11:18430200-18432000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:18430200-18432000	Weak transcription	GM12878-XiMat	blood
32	chr11:18430200-18433600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr11:18430200-18433600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr11:18430200-18433600	Weak transcription	Brain Germinal Matrix	brain
35	chr11:18430200-18433600	Weak transcription	HUVEC	blood vessel
36	chr11:18430200-18433800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:18430200-18433800	Weak transcription	Brain Substantia Nigra	brain
38	chr11:18430200-18433800	Weak transcription	Colon Smooth Muscle	Colon
39	chr11:18430200-18433800	Weak transcription	HSMMtube	muscle
40	chr11:18430200-18440200	Weak transcription	K562	blood
41	chr11:18430400-18432000	Weak transcription	Primary B cells from peripheral blood	blood
42	chr11:18430400-18432000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:18430400-18432200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:18430400-18432200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:18430400-18432200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:18430400-18433000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:18430400-18433400	Weak transcription	Placenta	Placenta
48	chr11:18430400-18433400	Weak transcription	Ovary	ovary
49	chr11:18430400-18433400	Weak transcription	HMEC	breast
50	chr11:18430400-18433600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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