Variant report

Variant	rs28639494
Chromosome Location	chr4:120512193-120512194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10003953	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010097	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10012406	1.00[AMR][1000 genomes]
rs10015714	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015999	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017842	1.00[AMR][1000 genomes]
rs10021318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023384	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027735	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028634	1.00[AMR][1000 genomes]
rs10029882	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031328	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032392	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213498	1.00[AMR][1000 genomes]
rs10471013	1.00[AMR][1000 genomes]
rs11098519	1.00[AMR][1000 genomes]
rs11098520	1.00[AMR][1000 genomes]
rs28380652	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28399227	1.00[AMR][1000 genomes]
rs28405434	1.00[AMR][1000 genomes]
rs28419430	1.00[AMR][1000 genomes]
rs28436005	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450144	1.00[AMR][1000 genomes]
rs28461667	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28469881	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470408	1.00[AMR][1000 genomes]
rs28535588	1.00[AMR][1000 genomes]
rs28576329	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28590285	1.00[AMR][1000 genomes]
rs28615474	1.00[AMR][1000 genomes]
rs28622207	1.00[AMR][1000 genomes]
rs28634062	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639769	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28651206	1.00[AMR][1000 genomes]
rs28654414	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665114	1.00[AMR][1000 genomes]
rs28669906	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709577	1.00[AMR][1000 genomes]
rs28736368	1.00[AMR][1000 genomes]
rs28864814	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28870820	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3872804	1.00[AMR][1000 genomes]
rs55905129	1.00[AMR][1000 genomes]
rs56191916	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57295141	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57516186	1.00[AMR][1000 genomes]
rs59116083	1.00[AMR][1000 genomes]
rs61729464	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61823285	1.00[AMR][1000 genomes]
rs72918555	1.00[AMR][1000 genomes]
rs72918590	1.00[AMR][1000 genomes]
rs72918597	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920607	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920619	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920685	1.00[AMR][1000 genomes]
rs9307478	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884290	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884542	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9993996	1.00[AMR][1000 genomes]
rs9996803	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998244	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120485800-120520000	Weak transcription	Small Intestine	intestine
2	chr4:120486600-120516600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:120486800-120515800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:120486800-120516400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:120486800-120527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:120492200-120513800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:120501800-120520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:120502000-120512400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:120502000-120516200	Weak transcription	Fetal Intestine Large	intestine
11	chr4:120502200-120516400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr4:120502200-120527800	Weak transcription	Pancreas	Pancrea
13	chr4:120502400-120526400	Weak transcription	Fetal Stomach	stomach
14	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
15	chr4:120503000-120517600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:120503200-120516400	Weak transcription	Ovary	ovary
17	chr4:120503200-120517800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:120504400-120516400	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:120504400-120520200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:120504600-120519800	Weak transcription	Fetal Intestine Small	intestine
21	chr4:120505000-120519800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:120505200-120518400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:120505400-120514400	Weak transcription	NH-A	brain
24	chr4:120505400-120516600	Weak transcription	Aorta	Aorta
25	chr4:120505600-120519800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:120506000-120514000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:120506000-120514000	Weak transcription	Fetal Lung	lung
28	chr4:120506000-120515400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:120506000-120516000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr4:120506200-120525800	Weak transcription	Fetal Kidney	kidney
31	chr4:120507000-120512800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:120507400-120512400	Weak transcription	Osteobl	bone
33	chr4:120509600-120520000	Weak transcription	Psoas Muscle	Psoas
34	chr4:120509800-120512800	Enhancers	Stomach Smooth Muscle	stomach
35	chr4:120510000-120512600	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr4:120510000-120513000	Enhancers	Colon Smooth Muscle	Colon
37	chr4:120510800-120512800	Genic enhancers	NHLF	lung
38	chr4:120511000-120513200	Enhancers	Rectal Smooth Muscle	rectum
39	chr4:120511000-120515800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:120511400-120512200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:120511400-120520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:120511600-120519600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:120512000-120512800	Weak transcription	Stomach Mucosa	stomach

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