Variant report

Variant	rs162131
Chromosome Location	chr5:7876751-7876752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7873979..7876833-chr5:7886025..7888380,2	K562	blood:
2	chr5:7875376..7880031-chr5:7885320..7890237,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10063685	0.80[CHB][hapmap]
rs10380	0.82[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs1046014	0.85[MEX][hapmap]
rs10520874	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12347	0.90[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs161870	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161871	0.96[TSI][hapmap];0.93[YRI][hapmap]
rs162026	0.90[CEU][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162028	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs162034	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs162035	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs162036	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162039	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162041	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16879305	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16879356	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16879410	1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.82[ASN][1000 genomes]
rs1994867	0.81[CHB][hapmap]
rs2277958	0.85[ASN][1000 genomes]
rs227872	0.82[CHB][hapmap]
rs2303081	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2640666	0.82[CHB][hapmap]
rs326118	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs326125	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs326210	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs327581	0.85[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap]
rs327586	0.84[ASN][1000 genomes]
rs327592	0.94[CHB][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4702507	0.82[CHB][hapmap];0.92[GIH][hapmap]
rs56219526	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57085915	0.83[ASN][1000 genomes]
rs57937475	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72716536	0.80[AMR][1000 genomes]
rs7727290	0.84[ASN][1000 genomes]
rs9332	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs162131	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs162131	MTRR	cis	parietal	SCAN
rs162131	MTRR	cis	lymphoblastoid	seeQTL
rs162131	MTRR	cis	Lymphoblastoid	GTEx
rs162131	FASTKD3	Cis_1M	lymphoblastoid	RTeQTL
rs162131	MTRR	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870200-7879800	Weak transcription	Pancreas	Pancrea
2	chr5:7870200-7882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:7870600-7878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:7870600-7878400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:7870800-7879800	Weak transcription	Colonic Mucosa	Colon
7	chr5:7871000-7894000	Weak transcription	Fetal Heart	heart
8	chr5:7871200-7903400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:7871200-7903600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:7871200-7903800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:7871400-7877800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:7871400-7878000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:7871400-7902400	Strong transcription	K562	blood
14	chr5:7871400-7903800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:7871600-7886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:7871600-7887200	Strong transcription	Fetal Thymus	thymus
17	chr5:7871600-7887600	Strong transcription	Placenta	Placenta
18	chr5:7871600-7902800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:7871600-7905000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:7871600-7906400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:7871600-7906800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:7871800-7876800	Strong transcription	A549	lung
23	chr5:7871800-7876800	Strong transcription	NHEK	skin
24	chr5:7871800-7884800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:7872000-7878200	Weak transcription	Psoas Muscle	Psoas
27	chr5:7872000-7886400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
29	chr5:7872200-7878000	Weak transcription	Fetal Intestine Small	intestine
30	chr5:7872800-7876800	Weak transcription	Small Intestine	intestine
31	chr5:7872800-7878000	Strong transcription	Fetal Intestine Large	intestine
32	chr5:7872800-7887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:7873000-7882200	Strong transcription	Fetal Lung	lung
34	chr5:7873200-7877000	Strong transcription	Liver	Liver
35	chr5:7873200-7878000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:7873200-7878000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:7873200-7903400	Strong transcription	Dnd41	blood
39	chr5:7873400-7878800	Strong transcription	Lung	lung
40	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
41	chr5:7873600-7878000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:7873600-7878200	Weak transcription	Right Ventricle	heart
43	chr5:7874000-7879200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:7874000-7879200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
47	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:7874200-7878400	Strong transcription	Primary B cells from cord blood	blood
49	chr5:7874200-7887000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr5:7874600-7876800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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