Variant report

Variant	rs10482605
Chromosome Location	chr5:142783521-142783522
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	RUNX3	chr5:142782574-142785511	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:142783433-142785544	GM12892	blood:	n/a	n/a
3	POLR2A	chr5:142783440-142785264	SK-N-SH	brain:	n/a	n/a
4	MAX	chr5:142781440-142785469	A549	lung:	n/a	chr5:142784085-142784095 chr5:142782756-142782766 chr5:142783623-142783633
5	RUNX3	chr5:142782899-142785421	GM12878	blood:	n/a	n/a
6	YY1	chr5:142783435-142783636	A549	lung:	n/a	chr5:142783533-142783547 chr5:142783621-142783630 chr5:142783532-142783546 chr5:142783530-142783541 chr5:142783526-142783540
7	NR2F2	chr5:142782460-142785308	MCF-7	breast:	n/a	n/a
8	CREB1	chr5:142782966-142785452	HepG2	liver:	n/a	n/a
9	POLR2A	chr5:142782015-142785534	Raji	blood:	n/a	n/a
10	MAX	chr5:142782994-142785396	SK-N-SH	brain:	n/a	chr5:142784085-142784095 chr5:142783623-142783633
11	YY1	chr5:142782902-142784121	GM12891	blood:	n/a	chr5:142784112-142784121 chr5:142783533-142783547 chr5:142783159-142783168 chr5:142783148-142783158 chr5:142783621-142783630 chr5:142783532-142783546 chr5:142784016-142784025 chr5:142783530-142783541 chr5:142783854-142783868 chr5:142783677-142783691 chr5:142784011-142784025 chr5:142783064-142783078 chr5:142783160-142783171 chr5:142783526-142783540
12	EP300	chr5:142783112-142785051	GM12878	blood:	n/a	chr5:142784117-142784126 chr5:142783698-142783714 chr5:142783856-142783872 chr5:142784014-142784023 chr5:142784114-142784123 chr5:142783539-142783548 chr5:142784236-142784250
13	MAZ	chr5:142781351-142785732	IMR90	lung:	n/a	chr5:142784085-142784095 chr5:142782756-142782766 chr5:142783623-142783633
14	MEF2C	chr5:142783010-142783950	GM12878	blood:	n/a	n/a
15	NR3C1	chr5:142783082-142783722	A549	lung:	n/a	n/a
16	FOXM1	chr5:142782727-142785429	GM12878	blood:	n/a	n/a
17	TCF7L2	chr5:142782132-142784429	HCT-116	colon:	n/a	n/a
18	CEBPB	chr5:142783070-142785166	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:142779195-142785402	GM12878	blood:	n/a	n/a
20	JUND	chr5:142782912-142784494	A549	lung:	n/a	chr5:142783232-142783241
21	GATA3	chr5:142779543-142785341	A549	lung:	n/a	chr5:142781692-142781713 chr5:142781699-142781708 chr5:142781698-142781708 chr5:142784454-142784463 chr5:142783912-142783921
22	RAD21	chr5:142783014-142785308	A549	lung:	n/a	chr5:142784270-142784280 chr5:142784982-142784994
23	FOXA2	chr5:142783123-142783806	A549	lung:	n/a	n/a
24	REST	chr5:142782533-142784000	A549	lung:	n/a	chr5:142783624-142783637 chr5:142783230-142783240 chr5:142782593-142782600
25	YY1	chr5:142782958-142783590	K562	blood:	n/a	chr5:142783533-142783547 chr5:142783159-142783168 chr5:142783148-142783158 chr5:142783532-142783546 chr5:142783530-142783541 chr5:142783064-142783078 chr5:142783160-142783171 chr5:142783526-142783540
26	ZNF143	chr5:142783084-142783837	K562	blood:	n/a	n/a
27	EBF1	chr5:142783155-142784032	GM12878	blood:	n/a	chr5:142783556-142783567
28	POLR2A	chr5:142781414-142785497	GM19099	blood:	n/a	n/a
29	NR3C1	chr5:142782899-142784191	A549	lung:	n/a	chr5:142784089-142784102
30	EBF1	chr5:142783202-142784033	GM12878	blood:	n/a	chr5:142783556-142783567
31	PML	chr5:142783484-142783721	GM12878	blood:	n/a	n/a
32	RAD21	chr5:142782996-142784636	SK-N-SH_RA	brain:	n/a	chr5:142784270-142784280
33	ZBTB7A	chr5:142782980-142785085	ECC-1	luminal epithelium:	n/a	n/a
34	CREB1	chr5:142782875-142785289	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:142782898-142784210	ProgFib	skin:	n/a	n/a
36	TAF1	chr5:142783504-142783716	GM12892	blood:	n/a	n/a
37	SIN3A	chr5:142781546-142785438	H1-hESC	embryonic stem cell:	n/a	chr5:142783743-142783754 chr5:142784644-142784657 chr5:142783626-142783637 chr5:142783624-142783637 chr5:142784366-142784379
38	MAX	chr5:142781498-142785442	K562	blood:	n/a	chr5:142784085-142784095 chr5:142782756-142782766 chr5:142783623-142783633
39	BRCA1	chr5:142783230-142783742	Hela-S3	cervix:	n/a	n/a
40	ZNF143	chr5:142783105-142785413	GM12878	blood:	n/a	chr5:142785333-142785351 chr5:142784837-142784847 chr5:142784059-142784077 chr5:142784653-142784671
41	CTCF	chr5:142783098-142784044	K562	blood:	n/a	n/a
42	POLR2A	chr5:142782824-142785417	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr5:142779252-142785530	Hela-S3	cervix:	n/a	n/a
44	RCOR1	chr5:142783117-142783811	GM12878	blood:	n/a	n/a
45	POLR2A	chr5:142782960-142784044	ECC-1	luminal epithelium:	n/a	n/a
46	RELA	chr5:142783010-142785511	GM15510	blood:	n/a	n/a
47	TBL1XR1	chr5:142783016-142785391	GM12878	blood:	n/a	n/a
48	SP1	chr5:142782222-142785565	A549	lung:	n/a	chr5:142784641-142784653 chr5:142784401-142784413 chr5:142783624-142783633 chr5:142782648-142782657 chr5:142782647-142782657 chr5:142783622-142783634 chr5:142784401-142784413 chr5:142782647-142782661 chr5:142782746-142782760 chr5:142784642-142784651 chr5:142783618-142783627 chr5:142784643-142784652 chr5:142784648-142784662 chr5:142784155-142784169 chr5:142784402-142784412 chr5:142782911-142782918 chr5:142784402-142784412 chr5:142783811-142783818 chr5:142783622-142783634 chr5:142784085-142784099 chr5:142784402-142784411 chr5:142783623-142783632 chr5:142784403-142784412
49	CHD2	chr5:142782017-142785410	GM12878	blood:	n/a	chr5:142784616-142784626 chr5:142782790-142782800 chr5:142784896-142784906 chr5:142782987-142782997
50	MAZ	chr5:142781578-142785519	K562	blood:	n/a	chr5:142784085-142784095 chr5:142782756-142782766 chr5:142783623-142783633

No.	Distal block	Cell Line	Cell type
1	chr5:142585827..142588456-chr5:142781871..142784934,4	K562	blood:
2	chr11:118965698..118966696-chr5:142783034..142783699,2	HCT-116	colon:
3	chr4:37687256..37688026-chr5:142783195..142783738,2	Hela-S3	cervix:
4	chr5:142779754..142782686-chr5:142783184..142785166,2	MCF-7	breast:
5	chr5:142767452..142770135-chr5:142781692..142784604,3	K562	blood:
6	chr5:140965764..140967390-chr5:142782677..142784677,2	K562	blood:

Variant related genes	Relation type
NR3C1	TF binding region
ENSG00000188486	Chromatin interaction
ENSG00000181826	Chromatin interaction
ENSG00000145819	Chromatin interaction
ENSG00000131504	Chromatin interaction
ENSG00000113580	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10076665	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10482633	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10482642	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10482689	0.83[AMR][1000 genomes]
rs10482700	0.83[AMR][1000 genomes]
rs10515521	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11740747	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11740792	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1438731	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17287758	0.83[AMR][1000 genomes]
rs17339831	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4128428	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72801052	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72801070	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72801079	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72801081	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72801083	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72801086	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72801088	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv882994	chr5:142770135-142791677	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3471370	chr5:142778742-142786304	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv3471371	chr5:142778742-142786304	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv3356658	chr5:142781784-142785332	Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv3364964	chr5:142781834-142785182	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10482605	NR3C1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142775400-142785200	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr5:142775400-142785600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:142775600-142785400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr5:142775600-142785600	Active TSS	Brain Angular Gyrus	brain
5	chr5:142776000-142785600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:142776200-142785400	Active TSS	Brain Substantia Nigra	brain
7	chr5:142777200-142785600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:142778200-142785600	Active TSS	Right Ventricle	heart
9	chr5:142779200-142785400	Active TSS	Lung	lung
10	chr5:142779200-142785600	Active TSS	Colonic Mucosa	Colon
11	chr5:142779800-142785400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:142779800-142785600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:142780000-142785400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:142780000-142785400	Active TSS	NHLF	lung
15	chr5:142780000-142785600	Active TSS	HSMMtube	muscle
16	chr5:142780200-142784200	Active TSS	NHEK	skin
17	chr5:142780200-142784400	Active TSS	Fetal Muscle Trunk	muscle
18	chr5:142780200-142784400	Active TSS	Stomach Smooth Muscle	stomach
19	chr5:142780200-142784400	Active TSS	GM12878-XiMat	blood
20	chr5:142780200-142784400	Active TSS	HMEC	breast
21	chr5:142780200-142785200	Active TSS	A549	lung
22	chr5:142780200-142785400	Active TSS	Brain Cingulate Gyrus	brain
23	chr5:142780200-142785400	Active TSS	Ovary	ovary
24	chr5:142780200-142785400	Active TSS	Placenta Amnion	Placenta Amnion
25	chr5:142780200-142785600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:142780200-142785600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr5:142780200-142785600	Active TSS	Left Ventricle	heart
28	chr5:142780200-142785600	Active TSS	Psoas Muscle	Psoas
29	chr5:142780200-142785600	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr5:142780200-142785600	Active TSS	Right Atrium	heart
31	chr5:142780200-142785600	Active TSS	HSMM	muscle
32	chr5:142780400-142784400	Active TSS	Fetal Muscle Leg	muscle
33	chr5:142780400-142784600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:142780400-142784600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:142780400-142785200	Active TSS	NHDF-Ad	bronchial
36	chr5:142780400-142785400	Active TSS	Aorta	Aorta
37	chr5:142780600-142785600	Active TSS	Thymus	Thymus
38	chr5:142780800-142784400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:142780800-142784400	Active TSS	Muscle Satellite Cultured Cells	--
40	chr5:142780800-142785000	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr5:142780800-142785400	Active TSS	Hela-S3	cervix
42	chr5:142781000-142784400	Active TSS	Osteobl	bone
43	chr5:142781200-142785200	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr5:142781400-142785200	Active TSS	Gastric	stomach
45	chr5:142781400-142785400	Active TSS	Fetal Intestine Large	intestine
46	chr5:142781400-142785600	Active TSS	Esophagus	oesophagus
47	chr5:142781400-142785600	Active TSS	Pancreas	Pancrea
48	chr5:142781600-142784000	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr5:142781600-142784400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:142781600-142785000	Active TSS	Spleen	Spleen

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