Variant report

Variant	rs32959
Chromosome Location	chr5:80042055-80042056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10040849	0.87[ASN][1000 genomes]
rs11950902	1.00[ASN][1000 genomes]
rs13161245	0.89[CEU][hapmap]
rs1346463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1346464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1382539	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1382540	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1382543	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1478834	0.89[CEU][hapmap]
rs1620258	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1628627	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1643638	0.95[CEU][hapmap]
rs1643649	0.90[CEU][hapmap]
rs1643650	0.89[CEU][hapmap]
rs1643651	1.00[ASN][1000 genomes]
rs1643657	0.89[CEU][hapmap]
rs1643658	0.89[CEU][hapmap]
rs1643659	0.89[CEU][hapmap]
rs1650648	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1650650	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650651	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650652	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs1650653	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650654	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650658	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650663	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650665	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650666	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650667	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650670	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1650688	0.88[ASN][1000 genomes]
rs1650692	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs1650709	0.89[CEU][hapmap]
rs1650737	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1650742	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1650747	1.00[ASN][1000 genomes]
rs1650749	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1650750	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677626	0.89[CEU][hapmap]
rs1677628	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1677629	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1677630	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677635	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs1677636	0.89[CEU][hapmap]
rs1677638	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1677639	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs1677641	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs1677643	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1677645	1.00[JPT][hapmap]
rs1677650	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1677652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677654	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677655	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677691	0.89[CEU][hapmap]
rs1677692	0.89[CEU][hapmap]
rs1677693	0.89[CEU][hapmap]
rs1677694	0.89[CEU][hapmap]
rs1677703	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1677707	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677709	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16878166	0.87[ASN][1000 genomes]
rs1824837	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1824838	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1824839	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs245331	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245332	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560424	0.89[CEU][hapmap]
rs2560425	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618369	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2618372	0.89[CEU][hapmap]
rs26267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26282	0.96[EUR][1000 genomes]
rs28027	0.95[EUR][1000 genomes]
rs2897262	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs6151614	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs6151615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6151618	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs6151619	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs6151620	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs6151665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6151770	1.00[ASN][1000 genomes]
rs6151838	0.87[ASN][1000 genomes]
rs73123307	0.88[ASN][1000 genomes]
rs73123310	1.00[ASN][1000 genomes]
rs73125413	0.87[ASN][1000 genomes]
rs73125416	0.87[ASN][1000 genomes]
rs73127211	0.80[ASN][1000 genomes]
rs836794	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs836795	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836798	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836799	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836800	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836801	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836804	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836808	0.94[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836809	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836810	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836816	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836818	0.89[CEU][hapmap]
rs836821	0.90[CEU][hapmap]
rs836822	0.89[CEU][hapmap]
rs836823	0.89[CEU][hapmap]
rs844368	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs844369	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844370	0.89[CEU][hapmap]
rs857016	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs861372	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs863214	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs863215	0.89[CEU][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs32959	DHFR	cis	Muscle Skeletal	GTEx
rs32959	DHFR	cis	Adipose Subcutaneous	GTEx
rs32959	DHFR	cis	Whole Blood	GTEx
rs32959	DHFR	cis	Heart Left Ventricle	GTEx
rs32959	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs32959	MSH3	cis	Whole Blood	GTEx
rs32959	MSH3	cis	Thyroid	GTEx
rs32959	ANKRD34B	cis	Whole Blood	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	chr5:80032400-80045400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:80032800-80043600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:80033200-80051400	Weak transcription	HMEC	breast
18	chr5:80034200-80049400	Strong transcription	Primary T cells from cord blood	blood
19	chr5:80034800-80050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:80035000-80050400	Weak transcription	Stomach Mucosa	stomach
21	chr5:80035200-80042200	Weak transcription	HSMMtube	muscle
22	chr5:80036400-80043800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr5:80037000-80042400	Strong transcription	Fetal Thymus	thymus
24	chr5:80037200-80049800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:80037200-80050600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:80037400-80042400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:80037400-80045800	Strong transcription	Liver	Liver
28	chr5:80037400-80049000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:80037400-80050600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:80037600-80044000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:80037600-80049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:80037600-80050200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr5:80038200-80043000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:80038200-80044400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:80038400-80043000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:80038400-80043200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr5:80038400-80043400	Strong transcription	HSMM	muscle
38	chr5:80038400-80043600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr5:80038400-80044000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:80038400-80044200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr5:80038400-80045800	Strong transcription	Adipose Nuclei	Adipose
42	chr5:80038600-80042200	Strong transcription	Fetal Kidney	kidney
43	chr5:80038600-80043200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:80039000-80042800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:80039000-80042800	Strong transcription	Fetal Lung	lung
46	chr5:80039200-80042600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:80039200-80043400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr5:80039200-80043400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:80039200-80045000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:80039200-80050200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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