Variant report

Variant	rs326124
Chromosome Location	chr5:7877178-7877179
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	chr5:7875376..7880031-chr5:7885320..7890237,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs162027	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs162030	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs162031	1.00[YRI][hapmap]
rs162032	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162037	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162038	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162040	0.88[AMR][1000 genomes]
rs162045	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs162048	0.94[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs162049	0.81[EUR][1000 genomes]
rs162051	0.83[AMR][1000 genomes]
rs162130	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs162270	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162272	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs162273	0.82[EUR][1000 genomes]
rs162448	0.80[CHB][hapmap]
rs16879452	0.82[ASN][1000 genomes]
rs1826541	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1994866	0.82[ASN][1000 genomes]
rs2077744	0.82[CEU][hapmap];0.80[CHB][hapmap];0.83[AMR][1000 genomes]
rs2613663	0.80[ASN][1000 genomes]
rs2613670	0.80[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2624228	0.81[ASN][1000 genomes]
rs2624229	0.81[ASN][1000 genomes]
rs2624230	0.81[ASN][1000 genomes]
rs2624231	0.80[ASN][1000 genomes]
rs2624237	0.84[JPT][hapmap]
rs2640664	0.81[ASN][1000 genomes]
rs2640665	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2966952	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs326120	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs326122	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs327573	0.84[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs327575	0.80[JPT][hapmap]
rs327582	0.83[ASN][1000 genomes]
rs49672	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs326124	MTRR	Cis_1M	lymphoblastoid	RTeQTL
rs326124	MTRR	cis	Temporal Cortex	GTEx
rs326124	MTRR	cis	Cerebellum	GTEx
rs326124	MTRR	cis	Frontal Cortex	GTEx
rs326124	MTRR	cis	Esophagus Muscularis	GTEx
rs326124	MTRR	cis	multi-tissue	Pritchard
rs326124	MTRR	cis	Brain Pons	GTEx

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	chr5:7871800-7884800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:7872000-7878200	Weak transcription	Psoas Muscle	Psoas
25	chr5:7872000-7886400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:7872000-7895200	Strong transcription	Fetal Muscle Leg	muscle
27	chr5:7872200-7878000	Weak transcription	Fetal Intestine Small	intestine
28	chr5:7872800-7878000	Strong transcription	Fetal Intestine Large	intestine
29	chr5:7872800-7887400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:7873000-7882200	Strong transcription	Fetal Lung	lung
31	chr5:7873200-7878000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:7873200-7878000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr5:7873200-7887600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:7873200-7903400	Strong transcription	Dnd41	blood
35	chr5:7873400-7878800	Strong transcription	Lung	lung
36	chr5:7873400-7904000	Strong transcription	Hela-S3	cervix
37	chr5:7873600-7878000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:7873600-7878200	Weak transcription	Right Ventricle	heart
39	chr5:7874000-7879200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:7874000-7879200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr5:7874000-7890800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:7874000-7905400	Strong transcription	Primary T cells from cord blood	blood
43	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:7874200-7878400	Strong transcription	Primary B cells from cord blood	blood
45	chr5:7874200-7887000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr5:7874600-7878200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr5:7874600-7894400	Strong transcription	Adipose Nuclei	Adipose
48	chr5:7874800-7879000	Strong transcription	Fetal Kidney	kidney
49	chr5:7874800-7881400	Strong transcription	Brain Germinal Matrix	brain
50	chr5:7874800-7887400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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