Variant report

Variant	rs2277037
Chromosome Location	chr5:80538143-80538144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10036376	0.86[CEU][hapmap]
rs10041138	0.83[CHB][hapmap]
rs10052929	0.85[CHB][hapmap]
rs10055018	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10071174	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10073527	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs10514215	0.86[CEU][hapmap];0.88[TSI][hapmap]
rs10514216	0.88[EUR][1000 genomes]
rs11960275	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12516414	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12652649	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12659947	0.90[JPT][hapmap]
rs13155580	0.85[CEU][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes]
rs13172928	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1566433	0.85[CHB][hapmap]
rs16876403	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16878586	0.90[JPT][hapmap]
rs17294956	0.86[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2270824	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291942	0.90[JPT][hapmap]
rs28819671	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4502795	0.89[CHB][hapmap]
rs4703828	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4703832	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4704709	0.94[EUR][1000 genomes]
rs4704714	0.85[CHB][hapmap]
rs4704716	0.90[JPT][hapmap]
rs4704717	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs545	0.91[CEU][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs57086010	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60434474	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6863732	0.85[CHB][hapmap]
rs6872183	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7448717	0.83[CEU][hapmap]
rs750728	0.86[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2763877	chr5:80535750-80545341	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv964904	chr5:80538090-80539221	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2277037	CTD-2248H3.1	cis	lung	GTEx
rs2277037	CTC-281B15.1	cis	lung	GTEx
rs2277037	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs2277037	CTC-281B15.1	cis	Thyroid	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
3	chr5:80529400-80540800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:80529400-80541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:80529400-80543400	Weak transcription	NHLF	lung
6	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:80529600-80541000	Weak transcription	Fetal Intestine Large	intestine
9	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:80530200-80541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:80530200-80544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:80530600-80542800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:80530600-80543000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:80530600-80543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:80530600-80544000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr5:80531000-80540200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:80531200-80538600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:80531200-80540000	Weak transcription	Aorta	Aorta
22	chr5:80531200-80542400	Weak transcription	Primary T cells from cord blood	blood
23	chr5:80531200-80551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
25	chr5:80531200-80564200	Weak transcription	HepG2	liver
26	chr5:80531400-80538200	Weak transcription	Pancreas	Pancrea
27	chr5:80531600-80542800	Weak transcription	Brain Germinal Matrix	brain
28	chr5:80531800-80538200	Weak transcription	HSMMtube	muscle
29	chr5:80531800-80541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:80531800-80543400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
32	chr5:80532000-80538800	Weak transcription	Gastric	stomach
33	chr5:80532000-80540800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:80532000-80541600	Weak transcription	Fetal Brain Female	brain
35	chr5:80532000-80542600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:80532000-80548400	Weak transcription	Lung	lung
37	chr5:80532200-80538400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:80532200-80548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:80532200-80551000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:80532200-80556800	Weak transcription	Dnd41	blood
41	chr5:80532400-80541800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:80532600-80545200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:80534800-80542400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:80535400-80541000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:80536000-80539200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr5:80536000-80541200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:80536000-80541200	Enhancers	Fetal Heart	heart
48	chr5:80536000-80542000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:80536200-80538200	Weak transcription	Brain Angular Gyrus	brain
50	chr5:80536200-80538400	Enhancers	Brain Anterior Caudate	brain

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