Variant report

Variant	rs9393554
Chromosome Location	chr6:24405768-24405769
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24400759..24404961-chr6:24405497..24410292,7	MCF-7	breast:
2	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
3	chr6:24282520..24284715-chr6:24405070..24407671,2	MCF-7	breast:
4	chr6:24404630..24407333-chr6:24559685..24561436,2	K562	blood:
5	chr6:24400786..24404823-chr6:24404929..24410869,7	K562	blood:

Variant related genes	Relation type
ENSG00000112293	Chromatin interaction
ENSG00000112294	Chromatin interaction
ENSG00000124532	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1056283	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1277343	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1321819	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13735	0.89[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1742282	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1772253	0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2753922	0.82[ASN][1000 genomes]
rs2793422	0.90[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2876672	0.82[ASN][1000 genomes]
rs3827640	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.97[ASN][1000 genomes]
rs6456612	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6920147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936856	0.84[ASN][1000 genomes]
rs7769012	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793652	0.87[ASN][1000 genomes]
rs793654	0.93[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs793657	0.82[ASN][1000 genomes]
rs793679	0.83[ASN][1000 genomes]
rs793680	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793682	0.85[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793684	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793686	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793687	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793688	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9393554	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs9393554	MRS2	cis	Whole Blood	GTEx
rs9393554	MRS2	cis	Esophagus Muscularis	GTEx
rs9393554	MRS2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:24402800-24405800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:24404000-24406000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
4	chr6:24404000-24406600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:24404000-24408000	Weak transcription	Aorta	Aorta
6	chr6:24404000-24408000	Weak transcription	Lung	lung
7	chr6:24404000-24408000	Weak transcription	Spleen	Spleen
8	chr6:24404000-24408800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:24404000-24413000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:24404200-24413000	Weak transcription	Gastric	stomach
11	chr6:24404400-24407600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:24404400-24412000	Weak transcription	Colonic Mucosa	Colon
13	chr6:24404400-24412400	Weak transcription	Fetal Brain Male	brain
14	chr6:24404400-24412800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:24404400-24412800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:24404400-24413000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:24404600-24405800	Genic enhancers	Dnd41	blood
18	chr6:24404600-24407600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:24404600-24407600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr6:24404600-24407600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr6:24404600-24407600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:24404600-24407600	Weak transcription	Placenta	Placenta
23	chr6:24404600-24407800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:24404600-24407800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:24404600-24407800	Weak transcription	HSMMtube	muscle
26	chr6:24404600-24407800	Weak transcription	NHLF	lung
27	chr6:24404600-24408000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:24404600-24408000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:24404600-24408000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:24404600-24408000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:24404600-24408000	Weak transcription	Left Ventricle	heart
32	chr6:24404600-24408000	Weak transcription	Ovary	ovary
33	chr6:24404600-24408000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:24404600-24408800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:24404600-24408800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:24404600-24408800	Weak transcription	NHDF-Ad	bronchial
37	chr6:24404600-24412400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:24404600-24412600	Weak transcription	Brain Substantia Nigra	brain
39	chr6:24404600-24412600	Weak transcription	Stomach Mucosa	stomach
40	chr6:24404600-24412600	Weak transcription	Thymus	Thymus
41	chr6:24404600-24413000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:24404600-24413000	Weak transcription	Small Intestine	intestine
43	chr6:24404600-24413600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:24404800-24405800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:24404800-24406400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:24404800-24407400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:24404800-24407600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:24404800-24407600	Weak transcription	Adipose Nuclei	Adipose
50	chr6:24404800-24408000	Weak transcription	HUVEC	blood vessel

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