Variant report

Variant	rs908668
Chromosome Location	chr19:56134038-56134039
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55994966..55997371-chr19:56133954..56136992,3	K562	blood:
2	chr19:56123945..56128950-chr19:56130054..56135521,12	K562	blood:
3	chr19:56133602..56135847-chr19:56151330..56154007,2	MCF-7	breast:
4	chr19:56115235..56119649-chr19:56131831..56136050,11	K562	blood:
5	chr19:56131862..56136924-chr19:56144839..56148352,5	MCF-7	breast:
6	chr19:56132811..56137423-chr19:56151241..56156557,5	MCF-7	breast:
7	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
8	chr19:56125033..56127900-chr19:56132851..56135429,4	MCF-7	breast:
9	chr19:56028711..56031331-chr19:56131776..56135542,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000173581	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12460543	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]
rs2280254	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2292810	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2292811	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34318926	0.85[ASN][1000 genomes]
rs34907477	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3852898	0.89[ASN][1000 genomes]
rs57314044	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751729	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs8110652	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs908668	ZNF583	cis	parietal	SCAN
rs908668	UBE2M	cis	cerebellum	SCAN
rs908668	ZNF256	cis	cerebellum	SCAN

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	chr19:56118400-56134400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:56118400-56135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:56118400-56135200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:56118400-56135200	Weak transcription	HUVEC	blood vessel
6	chr19:56118600-56134800	Strong transcription	Fetal Intestine Small	intestine
7	chr19:56118600-56134800	Weak transcription	K562	blood
8	chr19:56118600-56135200	Weak transcription	Fetal Brain Male	brain
9	chr19:56119600-56134800	Weak transcription	Hela-S3	cervix
10	chr19:56121200-56135000	Weak transcription	NH-A	brain
11	chr19:56121600-56135800	Weak transcription	NHDF-Ad	bronchial
12	chr19:56122200-56135800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:56122800-56135000	Weak transcription	HSMM	muscle
14	chr19:56123800-56134600	Strong transcription	Brain Germinal Matrix	brain
15	chr19:56128400-56135600	Weak transcription	Small Intestine	intestine
16	chr19:56129000-56135000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:56129000-56135200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:56129200-56134400	Weak transcription	Fetal Kidney	kidney
19	chr19:56129200-56134800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:56129200-56134800	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:56129200-56134800	Weak transcription	NHEK	skin
22	chr19:56129200-56135000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:56129200-56135000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr19:56129200-56135000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:56129200-56135000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:56129200-56135000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:56129200-56135000	Weak transcription	Stomach Mucosa	stomach
28	chr19:56129200-56135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:56129200-56135400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:56129200-56135400	Weak transcription	Colonic Mucosa	Colon
31	chr19:56129200-56135800	Weak transcription	Aorta	Aorta
32	chr19:56129200-56135800	Weak transcription	Brain Substantia Nigra	brain
33	chr19:56129400-56135000	Weak transcription	Osteobl	bone
34	chr19:56130600-56135200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr19:56130800-56134200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:56130800-56134600	Weak transcription	HSMMtube	muscle
37	chr19:56131000-56134200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:56131000-56134200	Strong transcription	Placenta	Placenta
39	chr19:56131000-56134600	Strong transcription	Fetal Stomach	stomach
40	chr19:56131400-56135000	Weak transcription	Adipose Nuclei	Adipose
41	chr19:56131600-56134200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:56131600-56134200	Strong transcription	Fetal Intestine Large	intestine
43	chr19:56131800-56134200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:56131800-56134200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr19:56131800-56134200	Enhancers	Primary T cells fromperipheralblood	blood
46	chr19:56132200-56134200	Strong transcription	Thymus	Thymus
47	chr19:56132200-56135800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:56132400-56134400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:56132400-56134400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:56132400-56134800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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