Variant report

Variant	rs701394
Chromosome Location	chr5:80296487-80296488
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	chr5:80284586..80286843-chr5:80294142..80297037,2	K562	blood:
2	chr5:80293956..80295842-chr5:80296253..80298015,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs484155	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs500676	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs517324	0.81[ASN][1000 genomes]
rs519871	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521135	0.83[JPT][hapmap]
rs541624	0.86[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv4897	chr5:80284196-80330223	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs701394	DHFR	cis	Muscle Skeletal	GTEx
rs701394	CKMT2	cis	cerebellum	SCAN
rs701394	ZCCHC9	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80286600-80299600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:80286800-80299800	Weak transcription	Brain Angular Gyrus	brain
3	chr5:80287200-80299800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:80288000-80299600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:80288200-80300000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:80288400-80297000	Weak transcription	Brain Hippocampus Middle	brain
7	chr5:80288800-80296800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:80288800-80299800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:80291400-80302400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr5:80292200-80299800	Weak transcription	HepG2	liver
11	chr5:80294600-80299800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:80294800-80298000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:80294800-80299600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:80294800-80299600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr5:80294800-80299800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:80294800-80299800	Weak transcription	Right Atrium	heart
17	chr5:80294800-80299800	Weak transcription	Thymus	Thymus
18	chr5:80294800-80302400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:80295000-80297000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:80295000-80297200	Enhancers	Primary T cells from cord blood	blood
21	chr5:80295000-80299800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:80295000-80300000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr5:80295800-80296600	Enhancers	Left Ventricle	heart
24	chr5:80295800-80296800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:80295800-80296800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:80295800-80297000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:80296000-80299600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:80296000-80299600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:80296000-80299600	Weak transcription	Fetal Thymus	thymus
30	chr5:80296000-80300200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr5:80296200-80298800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr5:80296200-80299800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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