Variant report

Variant	rs298096
Chromosome Location	chr5:59005938-59005939
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10061253	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1011644	0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1370230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs169869	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17742664	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1992112	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2164661	0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs256356	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2938784	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2938785	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2963824	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs297974	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs298054	0.84[ASN][1000 genomes]
rs298055	0.83[ASN][1000 genomes]
rs298057	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298058	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298059	0.91[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs298061	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298062	0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs298063	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs298067	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298072	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298074	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298075	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298076	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs298082	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs298083	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298084	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs298091	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs298092	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298093	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298097	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs402874	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4235477	0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs6450526	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6450527	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450529	0.91[ASN][1000 genomes]
rs6450531	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs6450532	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6865459	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6869459	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6875753	0.85[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs7701573	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7701748	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs905834	0.91[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv462190	chr5:58936943-59023870	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv598258	chr5:58936943-59023870	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1034283	chr5:58940594-59040762	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv537767	chr5:58940594-59040762	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
10	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv462191	chr5:58993297-59038610	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv598259	chr5:58993297-59038610	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58981200-59009000	Weak transcription	Hela-S3	cervix
2	chr5:58994800-59009000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:58999800-59009000	Weak transcription	Gastric	stomach
4	chr5:59000800-59008000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:59001000-59009000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:59003600-59007200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:59004200-59007400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:59004400-59007000	Enhancers	Fetal Lung	lung
9	chr5:59004800-59006200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:59004800-59006400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr5:59004800-59007600	Enhancers	Rectal Smooth Muscle	rectum
12	chr5:59005000-59006200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:59005000-59007000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:59005200-59006000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:59005200-59006000	Enhancers	Brain Angular Gyrus	brain
16	chr5:59005200-59006000	Enhancers	Brain Anterior Caudate	brain
17	chr5:59005200-59006000	Enhancers	Placenta	Placenta
18	chr5:59005200-59006200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:59005200-59006200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:59005200-59006200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:59005200-59006200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr5:59005200-59006200	Enhancers	Fetal Muscle Leg	muscle
23	chr5:59005200-59007000	Enhancers	Fetal Stomach	stomach
24	chr5:59005200-59007600	Enhancers	HSMMtube	muscle
25	chr5:59005400-59006000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:59005400-59006000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:59005400-59006000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr5:59005400-59006000	Enhancers	Brain Cingulate Gyrus	brain
29	chr5:59005400-59006000	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr5:59005400-59006000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr5:59005400-59006000	Enhancers	NHLF	lung
32	chr5:59005400-59006200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr5:59005400-59006200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:59005400-59006200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr5:59005400-59006600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr5:59005400-59006800	Enhancers	H9 Cell Line	embryonic stem cell
37	chr5:59005400-59007000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr5:59005400-59007000	Enhancers	HUVEC	blood vessel
39	chr5:59005400-59007600	Enhancers	HMEC	breast
40	chr5:59005600-59006000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr5:59005600-59006000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr5:59005600-59006000	Flanking Active TSS	Fetal Brain Male	brain
43	chr5:59005600-59006000	Enhancers	Fetal Heart	heart
44	chr5:59005600-59006000	Enhancers	Small Intestine	intestine
45	chr5:59005600-59006000	Enhancers	NH-A	brain
46	chr5:59005600-59006200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr5:59005600-59006200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr5:59005600-59006200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:59005600-59006200	Enhancers	NHDF-Ad	bronchial
50	chr5:59005600-59006400	Enhancers	Muscle Satellite Cultured Cells	--

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