Variant report

Variant	rs17243407
Chromosome Location	chr5:7858121-7858122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:7856421..7858362-chr5:7867413..7869187,3	MCF-7	breast:
2	chr5:7849544..7853202-chr5:7856682..7860407,3	K562	blood:
3	chr5:7853828..7855824-chr5:7856209..7859029,2	K562	blood:
4	chr5:7856634..7862841-chr5:7863423..7866521,7	MCF-7	breast:
5	chr5:7826263..7828308-chr5:7856719..7858613,3	K562	blood:
6	chr5:7856190..7858153-chr5:7870591..7872655,2	K562	blood:
7	chr5:7857476..7859602-chr5:7864063..7866187,3	K562	blood:

Variant related genes	Relation type
ENSG00000124279	Chromatin interaction
ENSG00000124275	Chromatin interaction
ENSG00000215217	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11949523	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12108985	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13154459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13181011	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13189728	0.89[EUR][1000 genomes]
rs13190084	0.89[EUR][1000 genomes]
rs16879109	1.00[CHD][hapmap]
rs17184211	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17267737	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2128266	0.89[EUR][1000 genomes]
rs34966478	0.89[EUR][1000 genomes]
rs62342527	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62342530	0.88[EUR][1000 genomes]
rs7716373	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9282787	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17243407	MTRR	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7851200-7859600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:7851400-7859600	Weak transcription	Esophagus	oesophagus
3	chr5:7851400-7860000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:7851600-7858200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:7851600-7859000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:7851600-7859200	Weak transcription	Fetal Brain Female	brain
7	chr5:7851600-7859800	Weak transcription	Psoas Muscle	Psoas
8	chr5:7851600-7859800	Weak transcription	Right Ventricle	heart
9	chr5:7851600-7860000	Weak transcription	Aorta	Aorta
10	chr5:7851600-7861600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:7851600-7861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:7851600-7865000	Weak transcription	Small Intestine	intestine
13	chr5:7851600-7866400	Weak transcription	Fetal Heart	heart
14	chr5:7851800-7859200	Weak transcription	HMEC	breast
15	chr5:7851800-7859600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:7851800-7861800	Weak transcription	Brain Substantia Nigra	brain
17	chr5:7851800-7868600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:7852200-7858200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:7852200-7867600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:7852200-7868400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:7852200-7868400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:7852200-7868400	Weak transcription	Gastric	stomach
23	chr5:7852200-7868600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:7852400-7859600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:7852400-7859800	Weak transcription	Spleen	Spleen
26	chr5:7852400-7861000	Weak transcription	HepG2	liver
27	chr5:7852400-7867800	Weak transcription	Fetal Brain Male	brain
28	chr5:7852600-7858600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:7852800-7858200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:7852800-7859200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:7852800-7859400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:7852800-7862000	Weak transcription	Lung	lung
33	chr5:7852800-7868400	Weak transcription	Pancreas	Pancrea
34	chr5:7853000-7858200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr5:7853000-7858600	Weak transcription	NHDF-Ad	bronchial
36	chr5:7853200-7858200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:7853200-7858400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:7853400-7860000	Weak transcription	Fetal Intestine Small	intestine
39	chr5:7853400-7861800	Weak transcription	Ovary	ovary
40	chr5:7853400-7862200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr5:7853600-7859600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:7854000-7861800	Weak transcription	HUVEC	blood vessel
43	chr5:7854000-7868400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:7855200-7858200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr5:7855200-7858400	Weak transcription	Brain Germinal Matrix	brain
46	chr5:7855200-7858600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:7855200-7859400	Weak transcription	Placenta	Placenta
48	chr5:7855200-7859600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:7855200-7859600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:7855400-7858200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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