Variant report

Variant	rs3756439
Chromosome Location	chr5:7890055-7890056
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1384230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16879236	0.88[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs16879248	0.88[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes]
rs16879259	0.88[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs16879334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879455	0.96[EUR][1000 genomes]
rs2277957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303080	0.96[EUR][1000 genomes]
rs2303082	0.96[EUR][1000 genomes]
rs3776458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822444	0.87[AFR][1000 genomes]
rs59809395	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60817278	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv525097	chr5:7887109-7896511	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv518862	chr5:7887478-7896511	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3756439	MTRR	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
3	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:7871400-7902400	Strong transcription	K562	blood
7	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
14	chr5:7873200-7903400	Strong transcription	Dnd41	blood
15	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
16	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
18	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
20	chr5:7875000-7906600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:7875400-7895200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr5:7875400-7903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:7875400-7903800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr5:7875400-7904200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr5:7875400-7904400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr5:7875600-7904400	Strong transcription	Left Ventricle	heart
27	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:7878800-7890600	Strong transcription	NH-A	brain
29	chr5:7879200-7901800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:7879200-7906400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr5:7879600-7900600	Strong transcription	Primary B cells from cord blood	blood
32	chr5:7880000-7894400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr5:7880000-7903600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:7880200-7892000	Strong transcription	GM12878-XiMat	blood
35	chr5:7880200-7894200	Weak transcription	Stomach Mucosa	stomach
36	chr5:7880400-7906600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr5:7880600-7907000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr5:7880800-7903800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr5:7881000-7904400	Strong transcription	Fetal Intestine Large	intestine
40	chr5:7882200-7902200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:7882400-7898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:7882400-7905000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:7882600-7898600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:7883800-7894400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:7885200-7895200	Strong transcription	NHEK	skin
46	chr5:7885400-7904000	Strong transcription	A549	lung
47	chr5:7885400-7904800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:7886200-7893000	Weak transcription	Brain Germinal Matrix	brain
49	chr5:7886800-7894400	Weak transcription	Pancreas	Pancrea
50	chr5:7887200-7891600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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