Variant report

Variant	rs12493565
Chromosome Location	chr3:49937205-49937206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:49937086-49937883	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr3:49937188-49937708	K562	blood:	n/a	n/a
3	RAD21	chr3:49937191-49937618	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:49935827..49937610-chr3:49975872..49978554,2	K562	blood:
2	chr3:49933351..49938041-chr3:49938966..49942332,9	K562	blood:
3	chr3:49904537..49906285-chr3:49936889..49938764,2	K562	blood:
4	chr3:49839049..49842350-chr3:49936029..49940414,4	K562	blood:
5	chr3:49823044..49824946-chr3:49937035..49939087,2	MCF-7	breast:
6	chr3:49927426..49930206-chr3:49934919..49938158,3	K562	blood:
7	chr3:49932972..49936126-chr3:49936946..49940007,3	MCF-7	breast:
8	chr3:49878485..49879205-chr3:49936998..49938153,4	MCF-7	breast:
9	chr3:49840382..49843169-chr3:49936309..49938239,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228008	TF binding region
MST1R	TF binding region
ENSG00000228008	Chromatin interaction
ENSG00000176095	Chromatin interaction
ENSG00000164078	Chromatin interaction
ENSG00000185614	Chromatin interaction
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11130223	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130225	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130230	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130237	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130239	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130240	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11916261	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11916999	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11920034	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11923132	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11924670	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11924711	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11925156	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486470	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12486808	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486832	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12489386	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490944	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492291	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12494077	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12494172	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12494916	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12495114	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12495831	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629129	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629553	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629677	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12630917	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630959	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631248	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12631306	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631309	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12631608	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632751	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12636045	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12636669	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637222	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637457	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637681	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638046	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317215	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13326300	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2023951	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2023952	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28478136	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35333166	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs41291716	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55643042	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57009357	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57575459	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58025924	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58621288	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58766761	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59802870	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61263937	0.85[EUR][1000 genomes]
rs61491513	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61729114	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260717	0.84[EUR][1000 genomes]
rs62260756	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262060	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62262095	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262096	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262099	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262100	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262104	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262105	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262116	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262117	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262136	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62262138	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262144	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262145	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62262148	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263578	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62263580	0.92[EUR][1000 genomes]
rs62263584	0.92[EUR][1000 genomes]
rs62263586	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263588	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263590	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263591	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62263600	0.82[AMR][1000 genomes]
rs6797500	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813644	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9859813	0.96[EUR][1000 genomes];0.86[ASN][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:53 , 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	chr3:49924000-49937600	Strong transcription	Fetal Stomach	stomach
8	chr3:49924600-49937600	Weak transcription	K562	blood
9	chr3:49924800-49938200	Weak transcription	Right Ventricle	heart
10	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
11	chr3:49926600-49938400	Weak transcription	Aorta	Aorta
12	chr3:49927000-49938000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:49927400-49937600	Weak transcription	Placenta	Placenta
14	chr3:49927600-49940400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:49928600-49943000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:49929000-49938400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:49929600-49941200	Weak transcription	Ovary	ovary
18	chr3:49931400-49938400	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:49931400-49943600	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:49933200-49938200	Weak transcription	Adipose Nuclei	Adipose
21	chr3:49933400-49939600	Weak transcription	Fetal Brain Female	brain
22	chr3:49933800-49941400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:49934200-49938600	Weak transcription	Fetal Lung	lung
24	chr3:49934400-49941400	Weak transcription	Brain Angular Gyrus	brain
25	chr3:49935200-49937600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:49935400-49937400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:49935400-49937800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr3:49935400-49940000	Weak transcription	Spleen	Spleen
29	chr3:49935600-49937400	Weak transcription	HepG2	liver
30	chr3:49935800-49937600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:49936000-49937600	Enhancers	HMEC	breast
32	chr3:49936000-49939000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:49936200-49938800	Transcr. at gene 5' and 3'	NHEK	skin
34	chr3:49936200-49939000	Enhancers	Lung	lung
35	chr3:49936200-49941000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:49936400-49937600	Genic enhancers	Fetal Intestine Small	intestine
37	chr3:49936400-49940800	Enhancers	Pancreas	Pancrea
38	chr3:49936600-49937400	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr3:49936600-49937400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr3:49936600-49937800	Enhancers	Gastric	stomach
41	chr3:49936800-49937400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:49936800-49937400	Weak transcription	Esophagus	oesophagus
43	chr3:49936800-49937600	Enhancers	Fetal Intestine Large	intestine
44	chr3:49936800-49937600	Enhancers	A549	lung
45	chr3:49936800-49937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:49936800-49939600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:49937000-49937400	Enhancers	Colonic Mucosa	Colon
48	chr3:49937000-49937400	Weak transcription	Fetal Thymus	thymus
49	chr3:49937000-49940800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr3:49937200-49937400	Enhancers	Duodenum Mucosa	Duodenum

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