Variant report

Variant	rs2307116
Chromosome Location	chr5:7861985-7861986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:7856634..7862841-chr5:7863423..7866521,7	MCF-7	breast:
2	chr5:7861753..7863633-chr5:7874321..7876476,2	K562	blood:
3	chr5:7853734..7855921-chr5:7861727..7863291,2	K562	blood:
4	chr5:7860007..7862983-chr5:7864596..7866833,2	K562	blood:

Variant related genes	Relation type
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11134265	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12653464	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801394	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs326209	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3733784	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4277880	1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2307116	MTRR	cis	lymphoblastoid	seeQTL
rs2307116	FASTKD3	Cis_1M	lymphoblastoid	RTeQTL
rs2307116	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7851600-7865000	Weak transcription	Small Intestine	intestine
2	chr5:7851600-7866400	Weak transcription	Fetal Heart	heart
3	chr5:7851800-7868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:7852200-7867600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:7852200-7868400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:7852200-7868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:7852200-7868400	Weak transcription	Gastric	stomach
8	chr5:7852200-7868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:7852400-7867800	Weak transcription	Fetal Brain Male	brain
10	chr5:7852800-7862000	Weak transcription	Lung	lung
11	chr5:7852800-7868400	Weak transcription	Pancreas	Pancrea
12	chr5:7853400-7862200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:7854000-7868400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:7856000-7868400	Weak transcription	Stomach Mucosa	stomach
15	chr5:7856600-7867600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:7857600-7862800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:7857600-7863200	Strong transcription	Brain Hippocampus Middle	brain
18	chr5:7857600-7864200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:7857600-7867800	Strong transcription	Fetal Muscle Leg	muscle
20	chr5:7857800-7862400	Strong transcription	Left Ventricle	heart
21	chr5:7857800-7863000	Strong transcription	Primary B cells from cord blood	blood
22	chr5:7857800-7863000	Strong transcription	Brain Anterior Caudate	brain
23	chr5:7857800-7863000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr5:7857800-7863200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr5:7857800-7863400	Strong transcription	Dnd41	blood
26	chr5:7857800-7863800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr5:7857800-7865800	Strong transcription	Fetal Intestine Large	intestine
28	chr5:7857800-7866000	Strong transcription	Liver	Liver
29	chr5:7857800-7866200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr5:7857800-7866200	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr5:7857800-7866600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:7858000-7862400	Strong transcription	Fetal Lung	lung
33	chr5:7858000-7864000	Strong transcription	Adipose Nuclei	Adipose
34	chr5:7858000-7865200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:7858000-7866000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:7858000-7866600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:7858000-7867200	Strong transcription	HSMM	muscle
38	chr5:7858000-7867400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:7858200-7863800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr5:7858200-7866600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:7858200-7867600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:7858400-7863000	Strong transcription	Brain Germinal Matrix	brain
43	chr5:7858400-7863200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr5:7858400-7865600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:7858400-7866200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:7858400-7868200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr5:7858600-7862000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr5:7858600-7862600	Strong transcription	NHDF-Ad	bronchial
49	chr5:7858600-7863000	Strong transcription	Fetal Thymus	thymus
50	chr5:7858600-7863400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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