Variant report

Variant	rs12460543
Chromosome Location	chr19:56134778-56134779
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:56134460..56137185-chr19:56162633..56166165,3	K562	blood:
2	chr19:55994966..55997371-chr19:56133954..56136992,3	K562	blood:
3	chr19:56134733..56137004-chr19:56165358..56168098,3	MCF-7	breast:
4	chr19:56134501..56137412-chr19:56145689..56149345,6	K562	blood:
5	chr19:55969994..55973672-chr19:56134456..56137440,3	MCF-7	breast:
6	chr19:56123945..56128950-chr19:56130054..56135521,12	K562	blood:
7	chr19:55917750..55919374-chr19:56134333..56135966,2	K562	blood:
8	chr19:56134500..56138557-chr19:56151822..56155582,4	K562	blood:
9	chr19:56134221..56137618-chr19:56162633..56168532,10	K562	blood:
10	chr19:56133602..56135847-chr19:56151330..56154007,2	MCF-7	breast:
11	chr19:56110415..56112373-chr19:56134518..56138349,4	MCF-7	breast:
12	chr19:55986860..55989470-chr19:56134046..56136997,2	K562	blood:
13	chr19:56116188..56118514-chr19:56134480..56137487,3	MCF-7	breast:
14	chr19:56109378..56114662-chr19:56134412..56139001,15	K562	blood:
15	chr19:56115235..56119649-chr19:56131831..56136050,11	K562	blood:
16	chr19:55918880..55921412-chr19:56134337..56137770,3	MCF-7	breast:
17	chr19:56131862..56136924-chr19:56144839..56148352,5	MCF-7	breast:
18	chr19:56132811..56137423-chr19:56151241..56156557,5	MCF-7	breast:
19	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
20	chr19:56125033..56127900-chr19:56132851..56135429,4	MCF-7	breast:
21	chr19:56028711..56031331-chr19:56131776..56135542,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000090971	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000213015	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12981222	0.85[EUR][1000 genomes]
rs2280254	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292810	0.87[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292811	0.93[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34318926	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34907477	0.98[ASN][1000 genomes]
rs35763366	0.96[EUR][1000 genomes]
rs3786644	0.85[CEU][hapmap]
rs3786646	0.86[CEU][hapmap]
rs3852898	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57314044	0.97[ASN][1000 genomes]
rs751729	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs8110652	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs908668	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking 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	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
9	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
10	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
11	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 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	chr19:56118200-56135000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:56118400-56135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:56118400-56135200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:56118400-56135200	Weak transcription	HUVEC	blood vessel
5	chr19:56118600-56134800	Strong transcription	Fetal Intestine Small	intestine
6	chr19:56118600-56134800	Weak transcription	K562	blood
7	chr19:56118600-56135200	Weak transcription	Fetal Brain Male	brain
8	chr19:56119600-56134800	Weak transcription	Hela-S3	cervix
9	chr19:56121200-56135000	Weak transcription	NH-A	brain
10	chr19:56121600-56135800	Weak transcription	NHDF-Ad	bronchial
11	chr19:56122200-56135800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:56122800-56135000	Weak transcription	HSMM	muscle
13	chr19:56128400-56135600	Weak transcription	Small Intestine	intestine
14	chr19:56129000-56135000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:56129000-56135200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:56129200-56134800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr19:56129200-56134800	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:56129200-56134800	Weak transcription	NHEK	skin
19	chr19:56129200-56135000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr19:56129200-56135000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr19:56129200-56135000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:56129200-56135000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:56129200-56135000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr19:56129200-56135000	Weak transcription	Stomach Mucosa	stomach
25	chr19:56129200-56135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:56129200-56135400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:56129200-56135400	Weak transcription	Colonic Mucosa	Colon
28	chr19:56129200-56135800	Weak transcription	Aorta	Aorta
29	chr19:56129200-56135800	Weak transcription	Brain Substantia Nigra	brain
30	chr19:56129400-56135000	Weak transcription	Osteobl	bone
31	chr19:56130600-56135200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr19:56131400-56135000	Weak transcription	Adipose Nuclei	Adipose
33	chr19:56132200-56135800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:56132400-56134800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:56132400-56134800	Weak transcription	Fetal Heart	heart
36	chr19:56132400-56135000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:56132400-56135200	Weak transcription	Right Atrium	heart
38	chr19:56132600-56134800	Weak transcription	Dnd41	blood
39	chr19:56132600-56135000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr19:56132800-56134800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:56132800-56134800	Weak transcription	Brain Angular Gyrus	brain
42	chr19:56132800-56135000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:56132800-56135000	Weak transcription	Brain Anterior Caudate	brain
44	chr19:56132800-56135200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:56132800-56135200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:56132800-56135200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:56132800-56135200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:56132800-56135200	Weak transcription	Psoas Muscle	Psoas
49	chr19:56133000-56134800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:56133000-56134800	Weak transcription	Fetal Lung	lung

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