Variant report

Variant	rs4634384
Chromosome Location	chr5:142780697-142780698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr5:142779330-142781062	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:142779127-142781086	GM12892	blood:	n/a	n/a
3	POLR2A	chr5:142779141-142780826	GM12892	blood:	n/a	n/a
4	POLR2A	chr5:142779195-142785402	GM12878	blood:	n/a	n/a
5	GATA3	chr5:142779543-142785341	A549	lung:	n/a	chr5:142781692-142781713 chr5:142781699-142781708 chr5:142781698-142781708 chr5:142784454-142784463 chr5:142783912-142783921
6	TBP	chr5:142779770-142780807	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:142779252-142785530	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:142779140-142780754	GM12891	blood:	n/a	n/a
9	MAFK	chr5:142780111-142780707	Hela-S3	cervix:	n/a	n/a
10	ZNF263	chr5:142779656-142780741	HEK293-T-REx	kidney:	n/a	n/a
11	MXI1	chr5:142779591-142785567	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:142779108-142781163	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:142779086-142780939	GM12892	blood:	n/a	n/a
14	POLR2A	chr5:142779252-142781223	GM12878	blood:	n/a	n/a
15	NFATC1	chr5:142779879-142781885	GM12878	blood:	n/a	n/a
16	MYC	chr5:142780602-142780700	MCF10A-Er-Src	breast:	n/a	n/a
17	CHD1	chr5:142773618-142783370	GM12878	blood:	n/a	chr5:142782790-142782800 chr5:142782987-142782997
18	REST	chr5:142779512-142781230	A549	lung:	n/a	n/a
19	PML	chr5:142779356-142781057	GM12878	blood:	n/a	n/a
20	CHD1	chr5:142776892-142785610	IMR90	lung:	n/a	chr5:142784616-142784626 chr5:142782790-142782800 chr5:142784896-142784906 chr5:142782987-142782997
21	POLR2A	chr5:142780509-142780738	GM12891	blood:	n/a	n/a
22	POLR2A	chr5:142779082-142781164	GM12892	blood:	n/a	n/a
23	POLR2A	chr5:142779701-142780728	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:142780507-142783382	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr5:142780562-142780738	Hela-S3	cervix:	n/a	n/a
26	NFATC1	chr5:142779744-142782536	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:142779121-142781243	GM12878	blood:	n/a	n/a
28	TCF7L2	chr5:142780639-142780839	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr5:142779732-142785550	GM18505	blood:	n/a	n/a
30	E2F4	chr5:142780629-142780986	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr5:142779301-142785850	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr5:142778310-142785199	IMR90	lung:	n/a	n/a
33	RAD21	chr5:142779862-142781124	IMR90	lung:	n/a	n/a
34	MXI1	chr5:142780171-142781191	Hela-S3	cervix:	n/a	n/a
35	MTA3	chr5:142779561-142781174	GM12878	blood:	n/a	n/a
36	SP1	chr5:142779422-142780874	A549	lung:	n/a	n/a
37	MYC	chr5:142780286-142782145	MCF10A-Er-Src	breast:	n/a	n/a
38	MAX	chr5:142779505-142781248	A549	lung:	n/a	n/a
39	WRNIP1	chr5:142779297-142781059	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:142779719-142780890	GM12892	blood:	n/a	n/a
41	POLR2A	chr5:142779104-142780800	GM12891	blood:	n/a	n/a
42	MTA3	chr5:142780180-142782175	GM12878	blood:	n/a	n/a
43	POLR2A	chr5:142779828-142780982	MCF10A-Er-Src	breast:	n/a	n/a
44	POU2F2	chr5:142779768-142780754	GM12878	blood:	n/a	n/a
45	MXI1	chr5:142779645-142785588	IMR90	lung:	n/a	n/a
46	SPI1	chr5:142780590-142780972	HL-60	blood:	n/a	chr5:142780790-142780803 chr5:142780791-142780804
47	SPI1	chr5:142780655-142780875	GM12891	blood:	n/a	chr5:142780790-142780803 chr5:142780791-142780804
48	TCF12	chr5:142778962-142780724	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:142780693-142780743	K562	blood:	n/a
2	chr5:142780693-142780743	HCF	heart:	n/a
3	chr5:142780693-142780743	GM12891	blood:	n/a
4	chr5:142780693-142780743	SK-N-SH_RA	brain:	n/a
5	chr5:142780693-142780743	PFSK-1	brain:	n/a
6	chr5:142780693-142780743	AG10803	skin:	n/a
7	chr5:142780693-142780743	HepG2	liver:	n/a
8	chr5:142780693-142780743	HEK293	kidney:	embryo
9	chr5:142780693-142780743	PrEC	prostate:	n/a
10	chr5:142780693-142780743	CMK	blood:	n/a
11	chr5:142780693-142780743	HUVEC	blood vessel:	n/a
12	chr5:142780693-142780743	NH-A	brain:	n/a
13	chr5:142780693-142780743	U87	brain:	n/a
14	chr5:142780693-142780743	Hepatocyte	liver:	n/a
15	chr5:142780693-142780743	SAEC	small airway:	n/a
16	chr5:142780693-142780743	GM06990	blood:	n/a
17	chr5:142780693-142780743	HIPEpiC	eye:	n/a
18	chr5:142780693-142780743	Hela-S3	cervix:	n/a
19	chr5:142780693-142780743	BE2_C	brain:	n/a
20	chr5:142780693-142780743	MCF-7	breast:	n/a
21	chr5:142780693-142780743	Caco-2	colon:	n/a
22	chr5:142780693-142780743	ECC-1	luminal epithelium:	n/a
23	chr5:142780693-142780743	MCF10A-Er-Src	breast:	n/a
24	chr5:142780693-142780743	AoSMC	blood vessel:	n/a
25	chr5:142780693-142780743	GM12878	blood:	n/a
26	chr5:142780693-142780743	GM12892	blood:	n/a
27	chr5:142780693-142780743	HAEpiC	amniotic membrane:	n/a
28	chr5:142780693-142780743	ovcar-3	ovarian:	n/a
29	chr5:142780693-142780743	HPAEpiC	pulmonary alveolar:	n/a
30	chr5:142780693-142780743	NB4	blood:	n/a
31	chr5:142780693-142780743	BJ	skin:	n/a
32	chr5:142780693-142780743	AG09319	gingival:	n/a
33	chr5:142780693-142780743	SKMC	muscle:	n/a
34	chr5:142780693-142780743	AG09309	skin:	n/a
35	chr5:142780693-142780743	HCT-116	colon:	n/a
36	chr5:142780693-142780743	HMEC	breast:	n/a
37	chr5:142780693-142780743	AG04450	lung:	fetal
38	chr5:142780693-142780743	NHBE	bronchial:	n/a
39	chr5:142780693-142780743	SK-N-SH	brain:	n/a
40	chr5:142780693-142780743	Jurkat	blood:	n/a
41	chr5:142780693-142780743	HCM	heart:	n/a
42	chr5:142780693-142780743	GM19239	blood:	n/a
43	chr5:142780693-142780743	ProgFib	skin:	n/a
44	chr5:142780693-142780743	HNPCEpiC	eye:	n/a
45	chr5:142780693-142780743	IMR90	lung:	fetal
46	chr5:142780693-142780743	PANC-1	pancreas:	n/a
47	chr5:142780693-142780743	NHDF-neo	bronchial:	n/a
48	chr5:142780693-142780743	T-47D	breast:	n/a
49	chr5:142780693-142780743	HEEpiC	esophagus:	n/a
50	chr5:142780693-142780743	A549	lung:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:142766873..142770437-chr5:142777323..142782250,4	K562	blood:
2	chr5:142779754..142782686-chr5:142783184..142785166,2	MCF-7	breast:

No data

Variant related genes	Relation type
NR3C1	TF binding region
NR3C1	CpG island
ENSG00000113580	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10041520	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258747	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs258763	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs33383	0.91[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33388	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6191	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6877893	0.90[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7716360	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs852976	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs852980	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs852983	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs853180	0.90[JPT][hapmap]
rs853183	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4634384	NR3C1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142774400-142782600	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr5:142775400-142785200	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr5:142775400-142785600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:142775600-142785400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr5:142775600-142785600	Active TSS	Brain Angular Gyrus	brain
6	chr5:142775800-142782000	Flanking Active TSS	HUVEC	blood vessel
7	chr5:142776000-142785600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:142776200-142785400	Active TSS	Brain Substantia Nigra	brain
9	chr5:142777000-142782000	Flanking Active TSS	Liver	Liver
10	chr5:142777200-142785600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:142778200-142780800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:142778200-142782000	Flanking Active TSS	HepG2	liver
13	chr5:142778200-142785600	Active TSS	Right Ventricle	heart
14	chr5:142778400-142780800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr5:142778400-142781800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:142778800-142781200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
17	chr5:142778800-142781400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:142778800-142781400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr5:142779000-142781400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
20	chr5:142779000-142781600	Flanking Active TSS	Fetal Heart	heart
21	chr5:142779200-142781400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr5:142779200-142785400	Active TSS	Lung	lung
23	chr5:142779200-142785600	Active TSS	Colonic Mucosa	Colon
24	chr5:142779400-142781200	Enhancers	Stomach Mucosa	stomach
25	chr5:142779600-142780800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr5:142779600-142781400	Active TSS	Brain Anterior Caudate	brain
27	chr5:142779800-142780800	Flanking Active TSS	Hela-S3	cervix
28	chr5:142779800-142781200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:142779800-142781400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr5:142779800-142781800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
31	chr5:142779800-142785400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:142779800-142785600	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr5:142780000-142780800	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr5:142780000-142781000	Flanking Active TSS	NH-A	brain
35	chr5:142780000-142781400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:142780000-142781600	Weak transcription	Small Intestine	intestine
37	chr5:142780000-142782000	Flanking Active TSS	Fetal Lung	lung
38	chr5:142780000-142785400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:142780000-142785400	Active TSS	NHLF	lung
40	chr5:142780000-142785600	Active TSS	HSMMtube	muscle
41	chr5:142780200-142780800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr5:142780200-142781000	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr5:142780200-142781200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:142780200-142781200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:142780200-142781200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:142780200-142781400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr5:142780200-142781400	Weak transcription	Esophagus	oesophagus
48	chr5:142780200-142781400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr5:142780200-142781600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr5:142780200-142781600	Active TSS	Rectal Mucosa Donor 29	rectum

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