Variant report

Variant	rs11838079
Chromosome Location	chr12:65029982-65029983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65015218..65018137-chr12:65028300..65031254,2	K562	blood:
2	chr12:65023053..65026165-chr12:65027701..65030902,3	K562	blood:
3	chr12:65029173..65030793-chr12:65051618..65053248,2	MCF-7	breast:
4	chr12:65020670..65023700-chr12:65029685..65032659,3	MCF-7	breast:
5	chr12:65024701..65026859-chr12:65028365..65030970,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225195	Chromatin interaction
ENSG00000207546	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12304348	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304958	0.99[AFR][1000 genomes]
rs12314167	0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12321771	0.86[AFR][1000 genomes]
rs12322583	0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13377735	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17100505	0.87[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56165064	0.83[AFR][1000 genomes]
rs61228947	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh 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	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv438218	chr12:65017844-65037483	Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65006800-65031800	Weak transcription	Dnd41	blood
2	chr12:65018600-65035000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:65019800-65030600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:65019800-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:65021200-65031200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr12:65021400-65043400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:65021600-65030600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:65021800-65037000	Weak transcription	Adipose Nuclei	Adipose
9	chr12:65021800-65038000	Weak transcription	Ovary	ovary
10	chr12:65022400-65039600	Weak transcription	Osteobl	bone
11	chr12:65024000-65031200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:65024800-65031800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
14	chr12:65025200-65044000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr12:65025800-65031400	Enhancers	HepG2	liver
16	chr12:65026400-65043200	Weak transcription	Fetal Stomach	stomach
17	chr12:65026600-65030600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:65026800-65032400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:65027400-65030000	Enhancers	Aorta	Aorta
20	chr12:65027400-65030800	Weak transcription	Fetal Intestine Small	intestine
21	chr12:65027400-65032600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:65027400-65041800	Weak transcription	Spleen	Spleen
23	chr12:65027600-65030200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:65027600-65030800	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr12:65027600-65031000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:65027600-65031800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr12:65027600-65032600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:65027800-65031200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:65027800-65047600	Weak transcription	Psoas Muscle	Psoas
30	chr12:65028000-65032400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:65028000-65032600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:65028000-65036600	Weak transcription	Lung	lung
33	chr12:65028200-65030000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr12:65028200-65047400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:65028400-65030000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:65028400-65030200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:65028400-65030600	Enhancers	Colonic Mucosa	Colon
38	chr12:65028400-65030600	Weak transcription	Small Intestine	intestine
39	chr12:65028400-65030800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:65028400-65030800	Weak transcription	Gastric	stomach
41	chr12:65028400-65032000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:65028400-65032400	Weak transcription	Hela-S3	cervix
43	chr12:65028400-65037000	Weak transcription	HUVEC	blood vessel
44	chr12:65028400-65038600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:65028400-65047400	Weak transcription	NHDF-Ad	bronchial
46	chr12:65028400-65047400	Weak transcription	NHLF	lung
47	chr12:65028600-65030400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:65028600-65056400	Weak transcription	NHEK	skin
49	chr12:65028800-65030000	Enhancers	Primary B cells from peripheral blood	blood
50	chr12:65029000-65030600	Weak transcription	Stomach Mucosa	stomach

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