Variant report

Variant	rs2753916
Chromosome Location	chr6:24360230-24360231
allele	A/C
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	BHLHE40	chr6:24359895-24360519	GM12878	blood:	n/a	chr6:24360100-24360121
2	RELA	chr6:24359939-24360527	GM19099	blood:	n/a	n/a
3	EGR1	chr6:24360042-24360516	ECC-1	luminal epithelium:	n/a	n/a
4	MAZ	chr6:24359923-24360250	K562	blood:	n/a	chr6:24360097-24360113
5	MTA3	chr6:24359830-24360524	GM12878	blood:	n/a	n/a
6	TCF3	chr6:24360164-24360433	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:24360100-24360662	H1-neurons	neurons:	n/a	n/a
8	MYC	chr6:24360184-24360280	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr6:24359852-24360435	GM12892	blood:	n/a	chr6:24360076-24360089 chr6:24360074-24360092 chr6:24360076-24360089 chr6:24360075-24360091
10	TCF12	chr6:24359968-24360493	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr6:24360227-24360467	GM12878	blood:	n/a	chr6:24360286-24360297
12	JUND	chr6:24359913-24360516	A549	lung:	n/a	chr6:24360150-24360159
13	RUNX3	chr6:24359885-24360546	GM12878	blood:	n/a	n/a
14	EBF1	chr6:24359962-24360419	GM12878	blood:	n/a	n/a
15	USF1	chr6:24359821-24360731	ECC-1	luminal epithelium:	n/a	chr6:24360100-24360121
16	REST	chr6:24359958-24360717	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr6:24359899-24360606	SK-N-MC	brain:	n/a	n/a
18	ZBTB7A	chr6:24359832-24360533	ECC-1	luminal epithelium:	n/a	n/a
19	SP4	chr6:24359920-24360234	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr6:24359948-24360387	GM12878	blood:	n/a	chr6:24360097-24360113
21	HDAC2	chr6:24359835-24360628	MCF-7	breast:	n/a	n/a
22	CTCF	chr6:24359964-24360231	Spleen_OC	spleen:	n/a	chr6:24360076-24360089 chr6:24360074-24360092 chr6:24360076-24360089 chr6:24360075-24360091
23	CTCF	chr6:24359852-24360306	GM19238	blood:	n/a	chr6:24360076-24360089 chr6:24360074-24360092 chr6:24360076-24360089 chr6:24360075-24360091
24	PAX5	chr6:24359938-24360530	GM12878	blood:	n/a	n/a
25	NR3C1	chr6:24360020-24360461	A549	lung:	n/a	n/a
26	MYC	chr6:24359950-24360609	MCF-7	breast:	n/a	chr6:24360508-24360519 chr6:24360097-24360113 chr6:24360381-24360390
27	RAD21	chr6:24359797-24360360	A549	lung:	n/a	chr6:24360167-24360180
28	HMGN3	chr6:24359944-24360373	K562	blood:	n/a	n/a
29	EGR1	chr6:24359965-24360689	HCT-116	colon:	n/a	n/a
30	RAD21	chr6:24359915-24360232	SK-N-SH_RA	brain:	n/a	chr6:24360167-24360180
31	CTCF	chr6:24359960-24360246	GM13977	blood:	n/a	chr6:24360076-24360089 chr6:24360074-24360092 chr6:24360076-24360089 chr6:24360075-24360091
32	RAD21	chr6:24359779-24360496	H1-hESC	embryonic stem cell:	n/a	chr6:24360167-24360180
33	CREB1	chr6:24359921-24360628	A549	lung:	n/a	n/a
34	USF1	chr6:24359913-24360338	SK-N-SH_RA	brain:	n/a	chr6:24360100-24360121
35	USF1	chr6:24359876-24360245	H1-hESC	embryonic stem cell:	n/a	chr6:24360100-24360121
36	POLR2A	chr6:24360230-24360438	MCF10A-Er-Src	breast:	n/a	n/a
37	EGR1	chr6:24359937-24360482	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr6:24359900-24360267	A549	lung:	n/a	chr6:24360076-24360089 chr6:24360074-24360092 chr6:24360076-24360089 chr6:24360075-24360091
39	YY1	chr6:24359942-24360261	SK-N-SH_RA	brain:	n/a	n/a
40	EGR1	chr6:24360024-24360331	GM12878	blood:	n/a	n/a
41	FOXA2	chr6:24359914-24360459	A549	lung:	n/a	n/a
42	POLR2A	chr6:24360113-24360650	MCF-7	breast:	n/a	n/a
43	YY1	chr6:24359803-24360330	H1-hESC	embryonic stem cell:	n/a	n/a
44	TCF12	chr6:24360185-24360477	GM12878	blood:	n/a	n/a
45	CEBPB	chr6:24359976-24360268	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr6:24359863-24360457	GM12878	blood:	n/a	chr6:24360076-24360089 chr6:24360074-24360092 chr6:24360076-24360089 chr6:24360075-24360091
47	POLR2A	chr6:24360033-24360648	MCF-7	breast:	n/a	n/a
48	E2F6	chr6:24359886-24360742	A549	lung:	n/a	chr6:24360076-24360086 chr6:24360368-24360375 chr6:24360368-24360375 chr6:24360283-24360293 chr6:24360368-24360375
49	MAX	chr6:24359948-24360583	H1-hESC	embryonic stem cell:	n/a	chr6:24360508-24360519 chr6:24360097-24360113 chr6:24360381-24360390
50	POLR2A	chr6:24360135-24360574	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24341482..24343826-chr6:24359222..24360846,2	MCF-7	breast:
2	chr6:24283175..24284815-chr6:24359561..24361041,12	MCF-7	breast:
3	chr6:24281775..24284260-chr6:24359000..24360636,2	MCF-7	breast:
4	chr6:24282994..24284064-chr6:24359605..24360545,4	MCF-7	breast:

Variant related genes	Relation type
DCDC2	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1087266	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1277337	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1277348	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2792666	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793664	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793697	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793708	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793711	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793719	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs813227	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][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	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
2	esv3426241	chr6:24358398-24360946	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3336385	chr6:24358423-24360671	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2753916	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24359000-24362800	Weak transcription	HepG2	liver
2	chr6:24359800-24360400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:24359800-24360400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:24359800-24360400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:24359800-24360400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:24359800-24360400	Active TSS	Brain Cingulate Gyrus	brain
7	chr6:24359800-24360400	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr6:24359800-24360400	Active TSS	Rectal Smooth Muscle	rectum
9	chr6:24359800-24360400	Active TSS	Right Atrium	heart
10	chr6:24359800-24360600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:24359800-24360600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:24359800-24360600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:24359800-24360600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:24359800-24360600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:24359800-24360600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:24359800-24360600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr6:24359800-24360600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr6:24359800-24360600	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr6:24359800-24360600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:24359800-24360600	Active TSS	Brain Angular Gyrus	brain
21	chr6:24359800-24360600	Active TSS	Brain Anterior Caudate	brain
22	chr6:24359800-24360600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:24359800-24360600	Active TSS	Fetal Intestine Small	intestine
24	chr6:24359800-24360600	Active TSS	Fetal Kidney	kidney
25	chr6:24359800-24360600	Active TSS	A549	lung
26	chr6:24359800-24360800	Active TSS	H9 Cell Line	embryonic stem cell
27	chr6:24359800-24360800	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr6:24359800-24360800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:24359800-24360800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:24359800-24360800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr6:24359800-24360800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:24359800-24360800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr6:24359800-24360800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:24359800-24360800	Active TSS	Fetal Brain Female	brain
35	chr6:24359800-24360800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr6:24359800-24360800	Active TSS	HSMM	muscle
37	chr6:24359800-24360800	Active TSS	NHLF	lung
38	chr6:24359800-24361000	Active TSS	NHEK	skin
39	chr6:24359800-24361000	Active TSS	Osteobl	bone
40	chr6:24360000-24360400	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr6:24360000-24360400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr6:24360000-24360400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr6:24360000-24360400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr6:24360000-24360400	Active TSS	Brain Hippocampus Middle	brain
45	chr6:24360000-24360400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr6:24360000-24360400	Active TSS	Brain Substantia Nigra	brain
47	chr6:24360000-24360400	Flanking Active TSS	Colonic Mucosa	Colon
48	chr6:24360000-24360400	Active TSS	Fetal Heart	heart
49	chr6:24360000-24360400	Active TSS	Pancreas	Pancrea
50	chr6:24360000-24360400	Active TSS	Rectal Mucosa Donor 29	rectum

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