Variant report

Variant	rs10477431
Chromosome Location	chr5:108124485-108124486
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10038669	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10044305	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10045220	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10060694	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062204	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10063167	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10073668	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs10079165	0.86[EUR][1000 genomes]
rs10515394	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12109934	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13180513	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2081126	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081129	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081130	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28637651	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2900035	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34125469	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35398495	0.87[AFR][1000 genomes]
rs4604227	0.80[ASN][1000 genomes]
rs4616948	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs6594335	0.88[JPT][hapmap]
rs6594338	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6594340	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6873068	0.89[AFR][1000 genomes]
rs6874229	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875320	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6880284	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6883442	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6889550	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6891194	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6895027	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7700630	0.81[ASN][1000 genomes]
rs7709267	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7710347	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7710482	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7712834	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7712956	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7723765	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7725263	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7725391	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726708	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7731891	0.86[EUR][1000 genomes]
rs7734520	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7735235	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9326747	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9326748	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9885082	0.82[ASN][1000 genomes]
rs9885168	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108090200-108127600	Weak transcription	NH-A	brain
2	chr5:108096400-108134000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:108098400-108128000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:108101600-108127600	Weak transcription	Osteobl	bone
5	chr5:108105400-108130600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:108105400-108133200	Weak transcription	NHDF-Ad	bronchial
7	chr5:108112600-108137200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:108117800-108138200	Weak transcription	Liver	Liver
9	chr5:108118000-108132800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:108118200-108126600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:108118200-108136800	Weak transcription	NHLF	lung
12	chr5:108120000-108136800	Weak transcription	A549	lung
13	chr5:108120200-108125600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:108120200-108137600	Weak transcription	Spleen	Spleen
15	chr5:108120200-108142200	Weak transcription	Aorta	Aorta
16	chr5:108120600-108146400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:108120800-108146400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr5:108121000-108138600	Weak transcription	Fetal Kidney	kidney
19	chr5:108121000-108139000	Weak transcription	Primary T cells from cord blood	blood
20	chr5:108121000-108139200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:108121200-108125800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:108121200-108126600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr5:108121200-108132200	Weak transcription	Fetal Lung	lung
24	chr5:108121200-108132800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:108121600-108124600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:108121800-108137200	Weak transcription	HSMMtube	muscle
27	chr5:108122800-108125000	Enhancers	Brain Substantia Nigra	brain
28	chr5:108123000-108138200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:108123400-108138200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr5:108123400-108139400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:108123600-108125000	Enhancers	Fetal Heart	heart
32	chr5:108123800-108124800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr5:108123800-108131000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:108124000-108124800	Enhancers	Stomach Smooth Muscle	stomach
35	chr5:108124000-108132600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:108124000-108133000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:108124000-108136000	Weak transcription	Fetal Intestine Large	intestine
38	chr5:108124000-108137200	Weak transcription	HSMM	muscle
39	chr5:108124000-108138800	Weak transcription	Fetal Brain Male	brain
40	chr5:108124000-108139200	Weak transcription	Primary B cells from cord blood	blood
41	chr5:108124200-108124600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr5:108124200-108125200	Enhancers	Brain Anterior Caudate	brain
43	chr5:108124200-108125200	Enhancers	Brain Hippocampus Middle	brain
44	chr5:108124200-108125200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr5:108124200-108125800	Weak transcription	Gastric	stomach
46	chr5:108124200-108125800	Weak transcription	Thymus	Thymus
47	chr5:108124200-108127400	Weak transcription	NHEK	skin
48	chr5:108124200-108128000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:108124200-108128200	Weak transcription	HMEC	breast
50	chr5:108124200-108128800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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