Variant report

Variant	rs56094988
Chromosome Location	chr3:98490449-98490450
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10428160	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10589669	0.80[EUR][1000 genomes]
rs11552978	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12107272	0.91[AMR][1000 genomes]
rs12108018	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12108142	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13059624	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13065136	0.83[AMR][1000 genomes]
rs13068317	0.91[AMR][1000 genomes]
rs13072410	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13074614	0.82[EUR][1000 genomes]
rs13076960	0.82[EUR][1000 genomes]
rs13080057	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13081992	0.91[AMR][1000 genomes]
rs13083238	0.82[EUR][1000 genomes]
rs13083613	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13083934	0.82[EUR][1000 genomes]
rs13084692	0.82[EUR][1000 genomes]
rs13087627	0.84[EUR][1000 genomes]
rs13087631	0.82[EUR][1000 genomes]
rs13088532	0.83[AMR][1000 genomes]
rs13091170	0.80[EUR][1000 genomes]
rs13091236	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13093128	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13096085	0.91[AMR][1000 genomes]
rs13097876	0.91[AMR][1000 genomes]
rs13100937	0.91[AMR][1000 genomes]
rs34008360	0.82[EUR][1000 genomes]
rs34279227	0.82[EUR][1000 genomes]
rs34284740	0.91[AMR][1000 genomes]
rs34470469	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34489202	0.84[EUR][1000 genomes]
rs34688367	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34711372	0.82[EUR][1000 genomes]
rs34725039	0.91[AMR][1000 genomes]
rs34826460	0.91[AMR][1000 genomes]
rs34848749	0.82[EUR][1000 genomes]
rs34860591	0.84[EUR][1000 genomes]
rs34951301	0.88[EUR][1000 genomes]
rs35006699	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35025156	0.91[AMR][1000 genomes]
rs35076733	0.80[EUR][1000 genomes]
rs35098355	0.82[EUR][1000 genomes]
rs35103318	0.91[AMR][1000 genomes]
rs35219252	0.82[EUR][1000 genomes]
rs35234681	0.91[AMR][1000 genomes]
rs35239055	0.82[EUR][1000 genomes]
rs35312318	0.91[AMR][1000 genomes]
rs35366262	0.82[EUR][1000 genomes]
rs35422064	0.82[EUR][1000 genomes]
rs35499232	0.91[AMR][1000 genomes]
rs35526367	0.91[AMR][1000 genomes]
rs35539438	0.84[EUR][1000 genomes]
rs35764973	0.91[AMR][1000 genomes]
rs35914268	0.82[EUR][1000 genomes]
rs35947806	0.82[EUR][1000 genomes]
rs36032715	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36175276	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41267851	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55644421	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56083233	0.83[AMR][1000 genomes]
rs56246599	0.91[AMR][1000 genomes]
rs6805362	0.82[EUR][1000 genomes]
rs71311393	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71311394	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71311397	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71311398	0.82[EUR][1000 genomes]
rs71311402	0.82[EUR][1000 genomes]
rs71313504	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71313508	0.91[AMR][1000 genomes]
rs71313509	0.91[AMR][1000 genomes]
rs71313510	0.91[AMR][1000 genomes]
rs71313511	0.91[AMR][1000 genomes]
rs7614053	0.91[AMR][1000 genomes];0.82[EUR][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98482200-98495800	Weak transcription	Dnd41	blood
3	chr3:98482400-98496000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:98482600-98494600	Weak transcription	Aorta	Aorta
5	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
6	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
8	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:98483600-98495200	Weak transcription	Fetal Thymus	thymus
11	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
12	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
13	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
18	chr3:98485000-98496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:98485400-98491600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:98487600-98490800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:98488000-98490800	Weak transcription	Liver	Liver
22	chr3:98488200-98496800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:98488600-98496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
26	chr3:98489200-98493200	Strong transcription	HUVEC	blood vessel
27	chr3:98489400-98491200	Strong transcription	HepG2	liver
28	chr3:98489600-98490600	Weak transcription	Left Ventricle	heart
29	chr3:98489600-98490600	Enhancers	HMEC	breast
30	chr3:98489600-98494400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:98489600-98497000	Weak transcription	Lung	lung
32	chr3:98489800-98494000	Weak transcription	Thymus	Thymus
33	chr3:98489800-98494600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:98489800-98494600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:98489800-98495200	Weak transcription	Pancreas	Pancrea
36	chr3:98489800-98495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:98489800-98496000	Weak transcription	Stomach Mucosa	stomach
38	chr3:98489800-98496200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:98489800-98496400	Weak transcription	Placenta	Placenta
40	chr3:98489800-98496600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:98489800-98496600	Weak transcription	Adipose Nuclei	Adipose
42	chr3:98489800-98497000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:98489800-98497400	Weak transcription	Right Ventricle	heart
44	chr3:98489800-98497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
46	chr3:98490000-98491200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr3:98490000-98494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:98490000-98495800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:98490000-98496200	Weak transcription	Brain Substantia Nigra	brain
50	chr3:98490000-98496400	Weak transcription	Brain Anterior Caudate	brain

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