Variant report

Variant	rs32985
Chromosome Location	chr5:80117918-80117919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80089229..80091065-chr5:80116335..80118690,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs152410	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152411	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs152412	0.91[EUR][1000 genomes]
rs152413	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245351	0.87[JPT][hapmap]
rs245363	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245377	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245390	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs245391	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs245392	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs245393	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs249635	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28059	0.88[CEU][hapmap]
rs32983	0.91[EUR][1000 genomes]
rs32986	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33008	0.96[CEU][hapmap];0.88[GIH][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap]
rs6151627	0.92[CEU][hapmap];0.81[GIH][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap]
rs6151629	0.91[CEU][hapmap]
rs6151653	0.92[CEU][hapmap];0.81[GIH][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap]
rs6151670	0.92[CEU][hapmap]
rs6887422	0.81[AFR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs32985	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs32985	DHFR	cis	Muscle Skeletal	GTEx
rs32985	JMY	cis	parietal	SCAN
rs32985	SCAMP1	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
2	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
3	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:80089400-80118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:80089600-80118400	Weak transcription	NHEK	skin
10	chr5:80089800-80118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:80090000-80118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:80090200-80118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:80090600-80124000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:80091400-80118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:80091400-80124600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:80091400-80124600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr5:80091400-80124600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
21	chr5:80091800-80125200	Weak transcription	Osteobl	bone
22	chr5:80093000-80124200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:80093800-80123800	Weak transcription	Pancreas	Pancrea
24	chr5:80094800-80124000	Weak transcription	GM12878-XiMat	blood
25	chr5:80096600-80118400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:80097000-80124400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:80097600-80121400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:80097600-80121600	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:80097800-80121600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:80098400-80121600	Weak transcription	Brain Anterior Caudate	brain
31	chr5:80099200-80121400	Weak transcription	Fetal Lung	lung
32	chr5:80100400-80118400	Weak transcription	HMEC	breast
33	chr5:80103000-80118400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:80103800-80118400	Weak transcription	Ovary	ovary
35	chr5:80103800-80144600	Weak transcription	Gastric	stomach
36	chr5:80106400-80119400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:80107200-80123800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:80108800-80118000	Weak transcription	Fetal Heart	heart
39	chr5:80109800-80119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:80109800-80121600	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:80110000-80123800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:80110000-80124800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:80110600-80118000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:80110600-80118600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr5:80110600-80124600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:80110600-80145200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:80110800-80119200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:80110800-80124200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:80110800-80124400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:80110800-80124600	Weak transcription	Placenta	Placenta

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