Variant report

Variant	rs9819888
Chromosome Location	chr3:49935503-49935504
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:49935440-49935590	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49933351..49938041-chr3:49938966..49942332,9	K562	blood:
2	chr3:49927426..49930206-chr3:49934919..49938158,3	K562	blood:
3	chr3:49931195..49934171-chr3:49934397..49936093,2	K562	blood:

Variant related genes	Relation type
MST1R	TF binding region
ENSG00000230698	TF binding region
ENSG00000164078	Chromatin interaction
ENSG00000228008	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12330297	1.00[AFR][1000 genomes]
rs13316958	0.87[AFR][1000 genomes]
rs13318943	1.00[AFR][1000 genomes]
rs13323932	0.87[AFR][1000 genomes]
rs13324545	1.00[AFR][1000 genomes]
rs55968312	1.00[AFR][1000 genomes]
rs9811223	0.87[AFR][1000 genomes]
rs9825944	1.00[AFR][1000 genomes]
rs9828683	1.00[AFR][1000 genomes]
rs9835029	1.00[AFR][1000 genomes]
rs9835838	0.87[AFR][1000 genomes]
rs9849605	1.00[AFR][1000 genomes]
rs9850145	0.87[AFR][1000 genomes]
rs9852055	0.86[AFR][1000 genomes]
rs9862830	1.00[AFR][1000 genomes]
rs9863339	1.00[AFR][1000 genomes]
rs9864231	1.00[AFR][1000 genomes]
rs9866016	1.00[AFR][1000 genomes]
rs9875038	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	47 gene(s)	inside rSNPs	diseases
4	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49919600-49937800	Weak transcription	Small Intestine	intestine
2	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
3	chr3:49920200-49938400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr3:49920400-49938200	Weak transcription	Left Ventricle	heart
5	chr3:49920600-49938200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:49920600-49938200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:49924000-49936000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:49924000-49937600	Strong transcription	Fetal Stomach	stomach
9	chr3:49924600-49937600	Weak transcription	K562	blood
10	chr3:49924800-49938200	Weak transcription	Right Ventricle	heart
11	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
12	chr3:49926600-49938400	Weak transcription	Aorta	Aorta
13	chr3:49927000-49938000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:49927400-49936800	Weak transcription	Fetal Thymus	thymus
15	chr3:49927400-49937600	Weak transcription	Placenta	Placenta
16	chr3:49927600-49940400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:49928600-49943000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:49929000-49938400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:49929600-49941200	Weak transcription	Ovary	ovary
20	chr3:49930800-49935800	Strong transcription	NHEK	skin
21	chr3:49931400-49936200	Strong transcription	Gastric	stomach
22	chr3:49931400-49938400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:49931400-49943600	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:49931800-49935800	Strong transcription	Hela-S3	cervix
25	chr3:49931800-49936400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:49931800-49936400	Strong transcription	Fetal Intestine Large	intestine
27	chr3:49931800-49936400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:49932000-49935600	Strong transcription	HMEC	breast
29	chr3:49932000-49935800	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr3:49932000-49936000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:49932400-49936400	Strong transcription	Fetal Intestine Small	intestine
32	chr3:49932400-49936400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:49932600-49935800	Strong transcription	Rectal Smooth Muscle	rectum
34	chr3:49932600-49936000	Strong transcription	Esophagus	oesophagus
35	chr3:49932600-49936000	Strong transcription	Lung	lung
36	chr3:49932600-49936200	Strong transcription	Colonic Mucosa	Colon
37	chr3:49933200-49938200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:49933400-49935600	Strong transcription	Stomach Mucosa	stomach
39	chr3:49933400-49939600	Weak transcription	Fetal Brain Female	brain
40	chr3:49933800-49941400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:49934200-49938600	Weak transcription	Fetal Lung	lung
42	chr3:49934400-49941400	Weak transcription	Brain Angular Gyrus	brain
43	chr3:49934600-49936400	Weak transcription	Pancreas	Pancrea
44	chr3:49934800-49936800	Weak transcription	A549	lung
45	chr3:49935000-49936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:49935200-49935600	Enhancers	HepG2	liver
47	chr3:49935200-49937600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:49935400-49936000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:49935400-49937200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:49935400-49937400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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