Variant report

Variant	rs176988
Chromosome Location	chr3:139244018-139244019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804665	0.83[EUR][1000 genomes]
rs10935330	1.00[CEU][hapmap]
rs1371340	0.86[EUR][1000 genomes]
rs1599744	0.86[EUR][1000 genomes]
rs167186	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16849065	0.86[EUR][1000 genomes]
rs16849083	1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176986	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211583	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs295491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295495	1.00[CEU][hapmap];0.86[AFR][1000 genomes]
rs4243399	0.83[EUR][1000 genomes]
rs4525826	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55735000	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56265838	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60144275	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61525084	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6439851	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6788313	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs72988746	0.90[EUR][1000 genomes]
rs7372667	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7372737	0.81[AMR][1000 genomes]
rs73868351	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7621965	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7636369	0.83[EUR][1000 genomes]
rs9824044	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9824195	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9838015	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9864352	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9864740	1.00[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:139223000-139247000	Weak transcription	Left Ventricle	heart
3	chr3:139228600-139245000	Weak transcription	Spleen	Spleen
4	chr3:139228800-139253200	Weak transcription	Gastric	stomach
5	chr3:139231000-139252800	Weak transcription	Right Ventricle	heart
6	chr3:139232400-139244400	Weak transcription	HSMMtube	muscle
7	chr3:139234400-139252600	Weak transcription	Lung	lung
8	chr3:139234800-139250600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:139234800-139251000	Weak transcription	Fetal Kidney	kidney
10	chr3:139234800-139251200	Weak transcription	Fetal Heart	heart
11	chr3:139235000-139253600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:139235200-139251400	Weak transcription	Liver	Liver
13	chr3:139236000-139245200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:139236400-139250800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:139236600-139245000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:139236600-139252000	Weak transcription	Right Atrium	heart
17	chr3:139237200-139249600	Weak transcription	Brain Germinal Matrix	brain
18	chr3:139238800-139251600	Weak transcription	Small Intestine	intestine
19	chr3:139239000-139245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:139239000-139247600	Weak transcription	NHEK	skin
21	chr3:139239000-139249600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:139239200-139244800	Weak transcription	Fetal Lung	lung
23	chr3:139239200-139247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:139239200-139251400	Weak transcription	Placenta	Placenta
25	chr3:139239400-139246400	Weak transcription	Esophagus	oesophagus
26	chr3:139239600-139250000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:139239600-139250000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:139239600-139251400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:139240600-139248600	Strong transcription	NH-A	brain
30	chr3:139240600-139251000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:139240800-139251800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:139241200-139245400	Weak transcription	Fetal Brain Female	brain
33	chr3:139241400-139251200	Strong transcription	Fetal Intestine Small	intestine
34	chr3:139241400-139251200	Strong transcription	Fetal Stomach	stomach
35	chr3:139241400-139253200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:139241600-139247600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:139241800-139245000	Weak transcription	Pancreas	Pancrea
38	chr3:139242000-139244200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
39	chr3:139242200-139244200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr3:139242200-139245000	Weak transcription	Aorta	Aorta
41	chr3:139242400-139244400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr3:139242400-139244400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:139243000-139244400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
44	chr3:139243400-139245600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr3:139243400-139246400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:139243800-139248600	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:139243800-139251000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:139243800-139252600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr3:139244000-139245200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:139244000-139247600	Genic enhancers	Ovary	ovary

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