Variant report

Variant	rs245336
Chromosome Location	chr5:80028301-80028302
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80024092..80025957-chr5:80026900..80028774,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs151886	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245009	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs245014	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245392	0.96[CEU][hapmap];0.81[YRI][hapmap]
rs245398	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245404	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs26780	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26781	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28059	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32951	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32953	0.94[EUR][1000 genomes]
rs32960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33008	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33011	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3776972	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40592	0.82[EUR][1000 genomes]
rs41097	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151627	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6151629	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6151653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6151670	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6151706	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151707	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7712332	0.90[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
rs245336	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs245336	DHFR	cis	Muscle Skeletal	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
2	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
6	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
7	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:80000200-80038600	Weak transcription	Esophagus	oesophagus
9	chr5:80000400-80036800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:80000400-80036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:80003600-80030400	Weak transcription	NHLF	lung
12	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
13	chr5:80009800-80039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:80010600-80036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:80010800-80032400	Weak transcription	Stomach Mucosa	stomach
16	chr5:80015800-80032400	Weak transcription	Pancreas	Pancrea
17	chr5:80016000-80038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:80016000-80040600	Weak transcription	Small Intestine	intestine
19	chr5:80016200-80040600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr5:80016200-80040600	Weak transcription	Colon Smooth Muscle	Colon
21	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:80016400-80032400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:80016400-80034200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:80016400-80038200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
26	chr5:80016600-80034200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:80020200-80043600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:80020800-80030800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr5:80021200-80031000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr5:80022200-80032200	Weak transcription	A549	lung
31	chr5:80022200-80040000	Weak transcription	K562	blood
32	chr5:80022600-80034000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:80022800-80038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:80022800-80038600	Weak transcription	Colonic Mucosa	Colon
35	chr5:80022800-80040600	Weak transcription	Spleen	Spleen
36	chr5:80022800-80041400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:80022800-80051200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:80023000-80030800	Weak transcription	Fetal Intestine Small	intestine
39	chr5:80023000-80031200	Weak transcription	Fetal Stomach	stomach
40	chr5:80023000-80032400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:80023000-80032400	Weak transcription	Gastric	stomach
42	chr5:80023000-80034200	Weak transcription	HSMMtube	muscle
43	chr5:80023000-80036800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:80023000-80038000	Weak transcription	Left Ventricle	heart
45	chr5:80023000-80038400	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:80023000-80038600	Weak transcription	Ovary	ovary
47	chr5:80023000-80038800	Weak transcription	Lung	lung
48	chr5:80023000-80040600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:80023000-80040600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr5:80023000-80040600	Weak transcription	Brain Hippocampus Middle	brain

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