Variant report

Variant	rs10075024
Chromosome Location	chr5:80132177-80132178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10040849	0.87[ASN][1000 genomes]
rs11951910	0.89[CEU][hapmap]
rs1346463	1.00[CHB][hapmap]
rs1346464	1.00[CHB][hapmap]
rs1650648	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1677652	1.00[CHB][hapmap]
rs1677653	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs16878166	0.87[ASN][1000 genomes]
rs1805353	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831684	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56103733	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61171552	0.81[AMR][1000 genomes]
rs6151615	1.00[CHB][hapmap]
rs6151665	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6151838	0.87[ASN][1000 genomes]
rs6151900	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151925	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151927	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151935	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73125413	0.87[ASN][1000 genomes]
rs73125416	0.87[ASN][1000 genomes]
rs73127211	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73137538	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139506	0.93[ASN][1000 genomes]
rs836801	1.00[CHB][hapmap]
rs836802	1.00[CHB][hapmap]
rs836806	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs836808	1.00[CHD][hapmap]
rs836813	1.00[CHB][hapmap]
rs863214	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs964584	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10075024	DHFR	cis	Whole Blood	GTEx
rs10075024	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs10075024	RASGRF2	cis	cerebellum	SCAN
rs10075024	DHFR	cis	Muscle Skeletal	GTEx
rs10075024	MSH3	cis	cerebellum	SCAN
rs10075024	DHFR	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
2	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
6	chr5:80103800-80144600	Weak transcription	Gastric	stomach
7	chr5:80110600-80145200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:80119000-80145000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:80120800-80143800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:80125000-80141600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr5:80125000-80141600	Weak transcription	Ovary	ovary
12	chr5:80125000-80142000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:80125000-80142000	Weak transcription	Fetal Stomach	stomach
14	chr5:80125000-80142200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:80125000-80142200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:80125000-80142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:80125000-80143600	Weak transcription	Left Ventricle	heart
18	chr5:80125000-80143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:80125000-80144600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:80125000-80145000	Weak transcription	Aorta	Aorta
21	chr5:80125200-80132600	Weak transcription	GM12878-XiMat	blood
22	chr5:80125200-80132800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:80125200-80133600	Weak transcription	Primary T cells from cord blood	blood
24	chr5:80125200-80141600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:80125200-80142000	Weak transcription	Fetal Intestine Small	intestine
26	chr5:80125200-80143800	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:80125200-80144200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr5:80125200-80144400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:80125200-80144400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:80125200-80145000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:80125200-80145000	Weak transcription	Adipose Nuclei	Adipose
32	chr5:80125200-80145400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr5:80125200-80151400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:80125200-80161600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:80125400-80141800	Weak transcription	Liver	Liver
36	chr5:80125400-80143800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:80125400-80144200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:80125400-80145000	Weak transcription	HepG2	liver
39	chr5:80125400-80145200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:80125600-80133600	Weak transcription	Primary B cells from cord blood	blood
41	chr5:80125600-80144200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:80125800-80143800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:80125800-80145000	Weak transcription	Fetal Lung	lung
44	chr5:80128000-80145400	Weak transcription	Brain Substantia Nigra	brain
45	chr5:80130200-80142000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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