Variant report

Variant	rs1172820
Chromosome Location	chr19:55815894-55815895
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55814981..55816687-chr19:56113260..56115264,2	MCF-7	breast:
2	chr19:55814784..55816804-chr19:55850965..55853492,2	K562	blood:
3	chr19:55814995..55818347-chr19:55916195..55920993,4	K562	blood:
4	chr19:55815541..55817130-chr19:55913347..55916145,2	K562	blood:
5	chr19:55811558..55817329-chr19:55895333..55899907,9	MCF-7	breast:
6	chr19:55811782..55819446-chr19:55894353..55900958,7	K562	blood:
7	chr19:55815584..55817619-chr19:55819921..55822145,2	MCF-7	breast:
8	chr19:55786801..55789660-chr19:55815741..55818613,2	K562	blood:
9	chr19:55814396..55817267-chr19:55897234..55899790,3	K562	blood:
10	chr19:55813052..55817410-chr19:55850511..55853343,6	MCF-7	breast:
11	chr19:55814792..55817559-chr19:55831323..55833407,2	K562	blood:
12	chr19:55808885..55818962-chr19:55893792..55900928,16	MCF-7	breast:
13	chr19:55815650..55817226-chr19:55918575..55920215,2	MCF-7	breast:
14	chr19:55813454..55816310-chr19:56151502..56153482,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180061	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000233493	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs7246479	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7252864	0.88[AMR][1000 genomes]
rs8113016	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats 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	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking 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	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv912458	chr19:55763409-55823822	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv912459	chr19:55791380-55845386	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS 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 target site	24 gene(s)	inside rSNPs	diseases
8	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
9	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55797000-55817800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:55797400-55824600	Weak transcription	Gastric	stomach
3	chr19:55811800-55817600	Weak transcription	Aorta	Aorta
4	chr19:55813200-55825200	Weak transcription	Left Ventricle	heart
5	chr19:55813200-55827600	Weak transcription	Lung	lung
6	chr19:55813400-55821600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:55813400-55825000	Strong transcription	Brain Germinal Matrix	brain
8	chr19:55813600-55816600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:55813600-55817200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:55813600-55817400	Weak transcription	Fetal Brain Male	brain
11	chr19:55813600-55817800	Weak transcription	Right Ventricle	heart
12	chr19:55813600-55819200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:55813600-55819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:55813600-55821200	Weak transcription	Pancreas	Pancrea
15	chr19:55813600-55821400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:55813600-55822000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:55813600-55822400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:55813600-55824800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:55813600-55827400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:55813600-55850000	Weak transcription	Right Atrium	heart
21	chr19:55813800-55816600	Weak transcription	Fetal Kidney	kidney
22	chr19:55813800-55816600	Weak transcription	K562	blood
23	chr19:55813800-55817200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr19:55813800-55817200	Weak transcription	Colonic Mucosa	Colon
25	chr19:55813800-55818000	Weak transcription	Fetal Intestine Large	intestine
26	chr19:55813800-55819200	Weak transcription	Ovary	ovary
27	chr19:55813800-55819800	Weak transcription	NHDF-Ad	bronchial
28	chr19:55813800-55820400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:55813800-55822000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:55813800-55822000	Strong transcription	Brain Hippocampus Middle	brain
31	chr19:55813800-55822600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:55813800-55823200	Strong transcription	Brain Angular Gyrus	brain
33	chr19:55813800-55824000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:55813800-55824000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr19:55813800-55824400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr19:55813800-55827600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:55814000-55816200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:55814000-55816200	Weak transcription	Fetal Thymus	thymus
39	chr19:55814000-55816600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:55814000-55816600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:55814000-55816600	Weak transcription	HSMM	muscle
42	chr19:55814000-55817400	Weak transcription	Primary T cells from cord blood	blood
43	chr19:55814000-55817400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:55814000-55818400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:55814000-55818400	Strong transcription	NHLF	lung
46	chr19:55814000-55818800	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr19:55814000-55819800	Weak transcription	GM12878-XiMat	blood
48	chr19:55814000-55821800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr19:55814000-55821800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr19:55814000-55822200	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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