Variant report

Variant	rs32960
Chromosome Location	chr5:80041918-80041919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs151886	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245009	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245014	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245392	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs245398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245404	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32951	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32953	0.92[EUR][1000 genomes]
rs33008	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33011	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3776972	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40592	0.81[EUR][1000 genomes]
rs41097	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6151629	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs6151653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs6151670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap]
rs6151706	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151707	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7712332	0.81[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs32960	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs32960	DHFR	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
4	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
5	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
7	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
9	chr5:80020200-80043600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:80022800-80051200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:80023000-80043000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:80023000-80043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:80024200-80046800	Weak transcription	Brain Angular Gyrus	brain
14	chr5:80024400-80043400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:80026000-80042000	Weak transcription	GM12878-XiMat	blood
16	chr5:80032400-80045400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:80032800-80043600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:80033200-80051400	Weak transcription	HMEC	breast
19	chr5:80034200-80049400	Strong transcription	Primary T cells from cord blood	blood
20	chr5:80034800-80050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:80035000-80050400	Weak transcription	Stomach Mucosa	stomach
22	chr5:80035200-80042200	Weak transcription	HSMMtube	muscle
23	chr5:80036400-80043800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr5:80037000-80042400	Strong transcription	Fetal Thymus	thymus
25	chr5:80037200-80049800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:80037200-80050600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr5:80037400-80042400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:80037400-80045800	Strong transcription	Liver	Liver
29	chr5:80037400-80049000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:80037400-80050600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr5:80037600-80044000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr5:80037600-80049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:80037600-80050200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:80038200-80043000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:80038200-80044400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:80038400-80043000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:80038400-80043200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:80038400-80043400	Strong transcription	HSMM	muscle
39	chr5:80038400-80043600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr5:80038400-80044000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:80038400-80044200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr5:80038400-80045800	Strong transcription	Adipose Nuclei	Adipose
43	chr5:80038600-80042200	Strong transcription	Fetal Kidney	kidney
44	chr5:80038600-80043200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:80039000-80042800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:80039000-80042800	Strong transcription	Fetal Lung	lung
47	chr5:80039200-80042000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr5:80039200-80042000	Weak transcription	Osteobl	bone
49	chr5:80039200-80042600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:80039200-80043400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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