Variant report

Variant	rs172363
Chromosome Location	chr5:58836207-58836208
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10056137	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10058879	0.91[EUR][1000 genomes]
rs159393	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs291118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs291120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs294480	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs294491	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs294503	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs295945	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs295949	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs295976	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs295977	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41404047	0.85[CHB][hapmap]

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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58822200-58838800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:58822800-58837600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58823000-58838200	Weak transcription	Fetal Brain Male	brain
4	chr5:58825000-58838600	Weak transcription	HSMMtube	muscle
5	chr5:58828800-58838800	Weak transcription	Gastric	stomach
6	chr5:58830400-58839000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:58834600-58838800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:58834600-58840600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr5:58834600-58840800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:58835000-58836400	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:58835000-58837400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr5:58835400-58836400	Weak transcription	Fetal Brain Female	brain
13	chr5:58835400-58840600	Enhancers	Brain Germinal Matrix	brain
14	chr5:58835600-58840600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:58835800-58836400	Enhancers	Psoas Muscle	Psoas
16	chr5:58835800-58837000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:58835800-58837000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr5:58835800-58837000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr5:58835800-58837200	Enhancers	Fetal Lung	lung
20	chr5:58835800-58839200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr5:58835800-58840200	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:58835800-58840200	Enhancers	Brain Hippocampus Middle	brain
23	chr5:58835800-58840400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:58835800-58840400	Enhancers	Brain Angular Gyrus	brain
25	chr5:58835800-58840400	Enhancers	Brain Anterior Caudate	brain
26	chr5:58835800-58840400	Enhancers	Brain Substantia Nigra	brain
27	chr5:58836000-58836400	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr5:58836000-58836600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:58836000-58836800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr5:58836000-58836800	Weak transcription	Fetal Stomach	stomach
31	chr5:58836000-58837600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:58836000-58840400	Enhancers	Duodenum Mucosa	Duodenum
33	chr5:58836200-58836400	Enhancers	Small Intestine	intestine
34	chr5:58836200-58836600	Flanking Active TSS	A549	lung
35	chr5:58836200-58836800	Enhancers	Rectal Smooth Muscle	rectum
36	chr5:58836200-58836800	Enhancers	Stomach Smooth Muscle	stomach
37	chr5:58836200-58837000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr5:58836200-58837200	Weak transcription	Stomach Mucosa	stomach
39	chr5:58836200-58837400	Weak transcription	Fetal Kidney	kidney

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