Variant report

Variant	rs16878166
Chromosome Location	chr5:80072602-80072603
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10040849	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075024	0.87[ASN][1000 genomes]
rs11950902	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11951910	0.89[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1346463	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1346464	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1620258	0.87[ASN][1000 genomes]
rs1643651	0.87[ASN][1000 genomes]
rs1650648	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs1650737	0.87[ASN][1000 genomes]
rs1650747	0.87[ASN][1000 genomes]
rs1650749	0.87[ASN][1000 genomes]
rs1650750	0.87[ASN][1000 genomes]
rs1677630	0.87[ASN][1000 genomes]
rs1677652	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1677653	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs1677654	0.87[ASN][1000 genomes]
rs1677655	0.87[ASN][1000 genomes]
rs1677707	0.87[ASN][1000 genomes]
rs1677709	0.87[ASN][1000 genomes]
rs1805353	0.87[ASN][1000 genomes]
rs245331	0.87[ASN][1000 genomes]
rs245332	0.87[ASN][1000 genomes]
rs2560425	0.87[ASN][1000 genomes]
rs2618369	0.87[ASN][1000 genomes]
rs26267	0.87[ASN][1000 genomes]
rs28831684	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs32959	0.87[ASN][1000 genomes]
rs56103733	0.87[ASN][1000 genomes]
rs6151615	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6151665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs6151770	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6151838	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151900	0.87[ASN][1000 genomes]
rs6151925	0.87[ASN][1000 genomes]
rs6151927	0.87[ASN][1000 genomes]
rs73123307	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73123310	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73125413	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125416	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127211	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73137538	0.87[ASN][1000 genomes]
rs73139506	0.80[ASN][1000 genomes]
rs836795	0.87[ASN][1000 genomes]
rs836798	0.87[ASN][1000 genomes]
rs836799	0.87[ASN][1000 genomes]
rs836800	0.87[ASN][1000 genomes]
rs836801	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs836802	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs836804	0.87[ASN][1000 genomes]
rs836806	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs836808	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs836809	0.87[ASN][1000 genomes]
rs836810	0.87[ASN][1000 genomes]
rs836813	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs836816	0.87[ASN][1000 genomes]
rs844368	0.87[ASN][1000 genomes]
rs844369	0.87[ASN][1000 genomes]
rs857016	0.87[ASN][1000 genomes]
rs861372	0.87[ASN][1000 genomes]
rs863214	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs964584	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16878166	ANKRD34B	cis	Whole Blood	GTEx
rs16878166	DHFR	cis	Heart Left Ventricle	GTEx
rs16878166	DHFR	cis	Muscle Skeletal	GTEx
rs16878166	RASGRF2	cis	cerebellum	SCAN
rs16878166	DP58	cis	multi-tissue	Pritchard
rs16878166	DHFR	cis	Whole Blood	GTEx
rs16878166	MSH3	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:80039200-80075800	Weak transcription	HepG2	liver
5	chr5:80040200-80073800	Weak transcription	Hela-S3	cervix
6	chr5:80041200-80076000	Weak transcription	Small Intestine	intestine
7	chr5:80041200-80100400	Weak transcription	Gastric	stomach
8	chr5:80041800-80094200	Weak transcription	NHLF	lung
9	chr5:80042200-80075800	Weak transcription	A549	lung
10	chr5:80042800-80073400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:80042800-80074800	Weak transcription	Fetal Stomach	stomach
12	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
13	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
14	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
15	chr5:80043000-80073600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr5:80043000-80075600	Weak transcription	Ovary	ovary
17	chr5:80043200-80075800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:80043400-80076200	Weak transcription	HUVEC	blood vessel
19	chr5:80043600-80089000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
21	chr5:80044400-80073600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:80048800-80088000	Weak transcription	Fetal Kidney	kidney
23	chr5:80049400-80089000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:80049600-80077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:80049800-80088800	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:80051000-80078600	Weak transcription	NHDF-Ad	bronchial
27	chr5:80051200-80073600	Weak transcription	Left Ventricle	heart
28	chr5:80051200-80075000	Weak transcription	Osteobl	bone
29	chr5:80051200-80077000	Weak transcription	NH-A	brain
30	chr5:80051200-80084000	Weak transcription	Thymus	Thymus
31	chr5:80051400-80073600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:80051600-80075800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:80051600-80088600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:80051600-80088800	Weak transcription	Colonic Mucosa	Colon
35	chr5:80051600-80095000	Weak transcription	Psoas Muscle	Psoas
36	chr5:80051800-80075000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:80051800-80089000	Weak transcription	HSMMtube	muscle
38	chr5:80052200-80095600	Weak transcription	Fetal Brain Male	brain
39	chr5:80052400-80075600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:80052400-80075800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr5:80052400-80085400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:80053000-80075800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:80053000-80088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr5:80054200-80073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:80056600-80075000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:80056800-80089000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:80057000-80085600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:80057200-80073200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:80057200-80075800	Weak transcription	Fetal Intestine Large	intestine
50	chr5:80057200-80083800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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