Variant report

Variant	rs1321819
Chromosome Location	chr6:24403039-24403040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:24402713-24404074	HepG2	liver:	n/a	n/a
2	GTF2F1	chr6:24403023-24403374	K562	blood:	n/a	n/a
3	REST	chr6:24402834-24403795	HepG2	liver:	n/a	chr6:24403613-24403626
4	RCOR1	chr6:24402864-24403974	K562	blood:	n/a	n/a
5	TCF7L2	chr6:24402914-24403676	Hela-S3	cervix:	n/a	n/a
6	TAF1	chr6:24402880-24403565	A549	lung:	n/a	n/a
7	POLR2A	chr6:24402935-24403769	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr6:24402881-24403691	K562	blood:	n/a	n/a
9	HDAC2	chr6:24402813-24403286	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr6:24402916-24403827	K562	blood:	n/a	n/a
11	MYC	chr6:24402880-24403849	K562	blood:	n/a	n/a
12	POLR2A	chr6:24402874-24403843	Hela-S3	cervix:	n/a	n/a
13	YY1	chr6:24402955-24403381	H1-hESC	embryonic stem cell:	n/a	chr6:24403010-24403021
14	PAX5	chr6:24402979-24403557	GM12878	blood:	n/a	n/a
15	PML	chr6:24402906-24403781	K562	blood:	n/a	n/a
16	HA-E2F1	chr6:24402846-24403826	MCF-7	breast:	n/a	chr6:24403131-24403141 chr6:24403129-24403138
17	TAF1	chr6:24403034-24403397	SK-N-SH	brain:	n/a	n/a
18	PML	chr6:24402870-24403571	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:24402927-24403690	K562	blood:	n/a	n/a
20	RCOR1	chr6:24402920-24403376	GM12878	blood:	n/a	n/a
21	YY1	chr6:24402947-24403437	HCT-116	colon:	n/a	chr6:24403010-24403021
22	MAX	chr6:24402946-24403870	A549	lung:	n/a	n/a
23	POLR2A	chr6:24402955-24403425	GM12891	blood:	n/a	n/a
24	RFX5	chr6:24402813-24403848	HepG2	liver:	n/a	chr6:24403729-24403746 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403476-24403485 chr6:24403473-24403488
25	TCF12	chr6:24403003-24403182	H1-hESC	embryonic stem cell:	n/a	n/a
26	ARID3A	chr6:24402992-24403188	K562	blood:	n/a	n/a
27	MAFK	chr6:24402649-24403438	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr6:24402864-24403443	SK-N-SH	brain:	n/a	n/a
29	JUND	chr6:24402907-24403613	K562	blood:	n/a	n/a
30	MAX	chr6:24402976-24403735	GM12878	blood:	n/a	n/a
31	YY1	chr6:24402938-24403725	HepG2	liver:	n/a	chr6:24403010-24403021
32	ZEB1	chr6:24402869-24403333	GM12878	blood:	n/a	chr6:24403031-24403042
33	POLR2A	chr6:24402909-24403489	U87	brain:	n/a	n/a
34	POLR2A	chr6:24402913-24403634	A549	lung:	n/a	n/a
35	ATF3	chr6:24402902-24403357	A549	lung:	n/a	n/a
36	TEAD4	chr6:24402763-24403289	A549	lung:	n/a	n/a
37	FOS	chr6:24402883-24403066	MCF10A-Er-Src	breast:	n/a	n/a
38	YY1	chr6:24403025-24403642	GM12892	blood:	n/a	n/a
39	REST	chr6:24402855-24403512	K562	blood:	n/a	n/a
40	SIX5	chr6:24403024-24403265	A549	lung:	n/a	n/a
41	POLR2A	chr6:24402934-24403677	A549	lung:	n/a	n/a
42	RFX5	chr6:24402643-24403772	Hela-S3	cervix:	n/a	chr6:24403729-24403746 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403730-24403745 chr6:24403476-24403485 chr6:24403473-24403488
43	CHD2	chr6:24402908-24403823	Hela-S3	cervix:	n/a	n/a
44	TAF1	chr6:24402929-24403792	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr6:24402930-24403794	GM12878	blood:	n/a	n/a
46	TAF1	chr6:24402948-24403710	Hela-S3	cervix:	n/a	n/a
47	NRF1	chr6:24402903-24403338	Hela-S3	cervix:	n/a	chr6:24403128-24403142 chr6:24403128-24403139
48	E2F6	chr6:24402963-24403755	K562	blood:	n/a	chr6:24403131-24403141 chr6:24403129-24403138
49	CBX3	chr6:24402913-24403844	K562	blood:	n/a	n/a
50	HEY1	chr6:24402843-24403839	HepG2	liver:	n/a	chr6:24403144-24403159

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
2	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:

Variant related genes	Relation type
MRS2	TF binding region
ENSG00000112294	Chromatin interaction
ENSG00000112293	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1056283	0.97[ASN][1000 genomes]
rs1277343	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13735	0.96[ASN][1000 genomes]
rs1742282	0.91[ASN][1000 genomes]
rs1772253	0.81[ASN][1000 genomes]
rs2753922	0.81[ASN][1000 genomes]
rs2793422	0.81[ASN][1000 genomes]
rs2876672	0.83[ASN][1000 genomes]
rs3827640	0.94[ASN][1000 genomes]
rs6456612	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6920147	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6936856	0.85[ASN][1000 genomes]
rs7769012	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793652	0.86[ASN][1000 genomes]
rs793654	0.81[ASN][1000 genomes]
rs793657	0.83[ASN][1000 genomes]
rs793680	0.94[ASN][1000 genomes]
rs793682	0.91[ASN][1000 genomes]
rs793684	0.91[ASN][1000 genomes]
rs793686	0.93[ASN][1000 genomes]
rs793687	0.93[ASN][1000 genomes]
rs793688	0.91[ASN][1000 genomes]
rs9393554	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[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
rs1321819	MRS2	cis	Esophagus Muscularis	GTEx
rs1321819	MRS2	cis	Whole Blood	GTEx
rs1321819	MRS2	cis	Heart Left Ventricle	GTEx
rs1321819	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24401800-24405400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:24402400-24403200	Active TSS	Brain Germinal Matrix	brain
3	chr6:24402400-24403200	Flanking Active TSS	Dnd41	blood
4	chr6:24402400-24406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr6:24402600-24403200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:24402600-24403200	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr6:24402600-24403400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:24402600-24403800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:24402600-24403800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:24402600-24404000	Active TSS	Brain Angular Gyrus	brain
11	chr6:24402600-24404000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr6:24402600-24404000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:24402600-24404200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:24402600-24404200	Active TSS	Brain Substantia Nigra	brain
15	chr6:24402600-24404200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:24402600-24404400	Active TSS	Brain Cingulate Gyrus	brain
17	chr6:24402600-24404400	Active TSS	A549	lung
18	chr6:24402600-24404600	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr6:24402600-24404600	Active TSS	Rectal Smooth Muscle	rectum
20	chr6:24402600-24404600	Active TSS	Stomach Smooth Muscle	stomach
21	chr6:24402600-24404800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:24402600-24405000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr6:24402600-24405200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:24402600-24405400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr6:24402600-24405600	Active TSS	GM12878-XiMat	blood
26	chr6:24402800-24403200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:24402800-24403200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:24402800-24403200	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr6:24402800-24403200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr6:24402800-24403200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr6:24402800-24403200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr6:24402800-24403200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:24402800-24403200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:24402800-24403200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:24402800-24403200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:24402800-24403200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:24402800-24403200	Flanking Active TSS	Colonic Mucosa	Colon
38	chr6:24402800-24403200	Active TSS	Fetal Brain Female	brain
39	chr6:24402800-24403200	Flanking Active TSS	Fetal Muscle Trunk	muscle
40	chr6:24402800-24403200	Flanking Active TSS	Placenta	Placenta
41	chr6:24402800-24403200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
42	chr6:24402800-24403200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr6:24402800-24403200	Enhancers	Stomach Mucosa	stomach
44	chr6:24402800-24403200	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr6:24402800-24403200	Flanking Active TSS	HUVEC	blood vessel
46	chr6:24402800-24403200	Flanking Active TSS	NHDF-Ad	bronchial
47	chr6:24402800-24403200	Flanking Active TSS	Osteobl	bone
48	chr6:24402800-24403400	Active TSS	Primary B cells from cord blood	blood
49	chr6:24402800-24403600	Active TSS	Liver	Liver
50	chr6:24402800-24403800	Active TSS	Primary T cells from cord blood	blood

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