Variant report

Variant	rs838718
Chromosome Location	chr2:234296650-234296651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:83)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:83 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr2:234296249-234296838	A549	lung:	n/a	n/a
2	NFIC	chr2:234296467-234297227	HepG2	liver:	n/a	n/a
3	CEBPB	chr2:234296526-234296899	HepG2	liver:	n/a	n/a
4	NFIC	chr2:234296234-234296764	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr2:234296382-234297268	HepG2	liver:	n/a	chr2:234296408-234296418
6	SMC3	chr2:234296336-234296671	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr2:234296529-234296674	A549	lung:	n/a	n/a
8	BHLHE40	chr2:234296528-234297174	HepG2	liver:	n/a	n/a
9	CEBPD	chr2:234296520-234296958	HepG2	liver:	n/a	n/a
10	CTCF	chr2:234296640-234296790	BE2_C	brain:	n/a	n/a
11	HDAC2	chr2:234296501-234296963	HepG2	liver:	n/a	n/a
12	ARID3A	chr2:234296620-234297235	HepG2	liver:	n/a	n/a
13	EP300	chr2:234296259-234296651	SK-N-SH_RA	brain:	n/a	n/a
14	NR3C1	chr2:234296277-234296961	A549	lung:	n/a	n/a
15	MAFK	chr2:234296278-234296958	IMR90	lung:	n/a	chr2:234296441-234296458
16	NFIC	chr2:234296180-234296878	SK-N-SH	brain:	n/a	n/a
17	JUND	chr2:234296601-234297145	HepG2	liver:	n/a	n/a
18	MXI1	chr2:234295899-234297076	SK-N-SH	brain:	n/a	n/a
19	RAD21	chr2:234296497-234296891	HepG2	liver:	n/a	n/a
20	JUND	chr2:234296268-234296799	A549	lung:	n/a	n/a
21	HNF4G	chr2:234296408-234297032	HepG2	liver:	n/a	chr2:234296759-234296774
22	RAD21	chr2:234296594-234296995	HepG2	liver:	n/a	n/a
23	REST	chr2:234296165-234296663	A549	lung:	n/a	n/a
24	MYBL2	chr2:234296398-234297094	HepG2	liver:	n/a	n/a
25	MYBL2	chr2:234296349-234297029	HepG2	liver:	n/a	n/a
26	CTCF	chr2:234296556-234296799	HepG2	liver:	n/a	n/a
27	SP1	chr2:234296419-234297230	HepG2	liver:	n/a	n/a
28	NR3C1	chr2:234296209-234297085	A549	lung:	n/a	n/a
29	FOXA2	chr2:234296274-234296703	A549	lung:	n/a	n/a
30	HEY1	chr2:234296446-234297005	HepG2	liver:	n/a	n/a
31	NFIC	chr2:234296001-234296957	SK-N-SH	brain:	n/a	n/a
32	RAD21	chr2:234296293-234296768	SK-N-SH_RA	brain:	n/a	n/a
33	RFX5	chr2:234296580-234297004	HepG2	liver:	n/a	n/a
34	SP1	chr2:234296026-234297044	A549	lung:	n/a	n/a
35	BCL3	chr2:234296008-234296949	A549	lung:	n/a	n/a
36	TCF12	chr2:234296281-234296849	A549	lung:	n/a	n/a
37	CREB1	chr2:234296284-234296832	A549	lung:	n/a	n/a
38	HNF4A	chr2:234296540-234297130	HepG2	liver:	n/a	chr2:234296759-234296774
39	TEAD4	chr2:234296435-234297061	HepG2	liver:	n/a	n/a
40	ELF1	chr2:234296601-234296937	HepG2	liver:	n/a	chr2:234296734-234296743
41	NFIC	chr2:234296587-234297244	HepG2	liver:	n/a	n/a
42	NR3C1	chr2:234296400-234296828	A549	lung:	n/a	n/a
43	GATA3	chr2:234296040-234297142	A549	lung:	n/a	n/a
44	MAFK	chr2:234296394-234297072	HepG2	liver:	n/a	chr2:234296441-234296458
45	MAX	chr2:234296014-234297018	A549	lung:	n/a	chr2:234296408-234296418
46	EP300	chr2:234295889-234297076	A549	lung:	n/a	n/a
47	MAX	chr2:234296454-234297091	HepG2	liver:	n/a	n/a
48	SP1	chr2:234296078-234297058	A549	lung:	n/a	n/a
49	EP300	chr2:234295984-234297022	A549	lung:	n/a	n/a
50	HNF4G	chr2:234296531-234296952	HepG2	liver:	n/a	chr2:234296759-234296774

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:234296642-234296692	AG04450	lung:	fetal
2	chr2:234296642-234296692	AG09309	skin:	n/a
3	chr2:234296642-234296692	LNCaP	prostate:	n/a
4	chr2:234296642-234296692	SAEC	small airway:	n/a
5	chr2:234296642-234296692	RPTEC	kidney:	n/a
6	chr2:234296642-234296692	GM12891	blood:	n/a
7	chr2:234296642-234296692	PFSK-1	brain:	n/a
8	chr2:234296642-234296692	HepG2	liver:	n/a
9	chr2:234296642-234296692	AG04449	skin:	fetal
10	chr2:234296642-234296692	AG10803	skin:	n/a
11	chr2:234296642-234296692	Hela-S3	cervix:	n/a
12	chr2:234296642-234296692	Hepatocyte	liver:	n/a
13	chr2:234296642-234296692	AG09319	gingival:	n/a
14	chr2:234296642-234296692	HPAEpiC	pulmonary alveolar:	n/a
15	chr2:234296642-234296692	HAEpiC	amniotic membrane:	n/a
16	chr2:234296642-234296692	IMR90	lung:	fetal
17	chr2:234296642-234296692	HRCEpiC	kidney:	n/a
18	chr2:234296642-234296692	CMK	blood:	n/a
19	chr2:234296642-234296692	HNPCEpiC	eye:	n/a
20	chr2:234296642-234296692	SK-N-SH_RA	brain:	n/a
21	chr2:234296642-234296692	BE2_C	brain:	n/a
22	chr2:234296642-234296692	HCF	heart:	n/a
23	chr2:234296642-234296692	HEEpiC	esophagus:	n/a
24	chr2:234296642-234296692	Jurkat	blood:	n/a
25	chr2:234296642-234296692	HIPEpiC	eye:	n/a
26	chr2:234296642-234296692	HMEC	breast:	n/a
27	chr2:234296642-234296692	GM12878	blood:	n/a
28	chr2:234296642-234296692	PANC-1	pancreas:	n/a
29	chr2:234296642-234296692	A549	lung:	n/a
30	chr2:234296642-234296692	MCF-7	breast:	n/a
31	chr2:234296642-234296692	NHBE	bronchial:	n/a
32	chr2:234296642-234296692	AoSMC	blood vessel:	n/a
33	chr2:234296642-234296692	SKMC	muscle:	n/a
34	chr2:234296642-234296692	MCF10A-Er-Src	breast:	n/a
35	chr2:234296642-234296692	SK-N-MC	brain:	n/a
36	chr2:234296642-234296692	HRE	kidney:	n/a
37	chr2:234296642-234296692	ProgFib	skin:	n/a
38	chr2:234296642-234296692	H1-hESC	embryonic stem cell:	embryo
39	chr2:234296642-234296692	HCT-116	colon:	n/a
40	chr2:234296642-234296692	GM19239	blood:	n/a
41	chr2:234296642-234296692	BJ	skin:	n/a
42	chr2:234296642-234296692	HRPEpiC	eye:	n/a
43	chr2:234296642-234296692	HCM	heart:	n/a
44	chr2:234296642-234296692	ECC-1	luminal epithelium:	n/a
45	chr2:234296642-234296692	U87	brain:	n/a
46	chr2:234296642-234296692	NT2-D1	testis:	n/a
47	chr2:234296642-234296692	GM12892	blood:	n/a
48	chr2:234296642-234296692	PrEC	prostate:	n/a
49	chr2:234296642-234296692	HL-60	blood:	n/a
50	chr2:234296642-234296692	NB4	blood:	n/a

No data

Variant related genes	Relation type
DGKD	TF binding region
DGKD	CpG island

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2971868	0.86[CHD][hapmap]
rs7422272	0.84[CHD][hapmap]
rs838707	0.83[CHB][hapmap]
rs838713	0.82[CHB][hapmap]
rs838714	0.87[CHB][hapmap]
rs838715	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs838719	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs838720	0.86[ASN][1000 genomes]
rs838722	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs838730	0.86[CHD][hapmap]
rs838731	0.84[CHD][hapmap]
rs838732	0.86[CHD][hapmap]
rs838733	0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs838718	USP40	cis	cerebellum	SCAN
rs838718	DGKD	Cis_1M	lymphoblastoid	RTeQTL
rs838718	DGKD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234264600-234307600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:234282400-234298000	Weak transcription	Dnd41	blood
6	chr2:234289000-234307600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:234290600-234297000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:234290800-234296800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:234291000-234297000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr2:234292000-234297200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:234292200-234297200	Enhancers	Fetal Heart	heart
12	chr2:234292200-234297200	Enhancers	Left Ventricle	heart
13	chr2:234292400-234296800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:234292400-234297200	Enhancers	Right Ventricle	heart
15	chr2:234292600-234297000	Enhancers	Fetal Stomach	stomach
16	chr2:234292600-234297000	Enhancers	Fetal Thymus	thymus
17	chr2:234292600-234298400	Enhancers	Fetal Muscle Leg	muscle
18	chr2:234292800-234296800	Enhancers	Esophagus	oesophagus
19	chr2:234293000-234297000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:234293200-234307600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:234293400-234297200	Enhancers	Brain Angular Gyrus	brain
22	chr2:234293400-234297200	Enhancers	Right Atrium	heart
23	chr2:234293600-234297200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr2:234293800-234308000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:234293800-234308000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:234294000-234297200	Enhancers	Fetal Brain Male	brain
27	chr2:234294200-234306600	Weak transcription	HMEC	breast
28	chr2:234294600-234297200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr2:234294600-234298200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:234294600-234318800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:234294800-234296800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:234294800-234296800	Enhancers	Gastric	stomach
33	chr2:234294800-234296800	Flanking Active TSS	A549	lung
34	chr2:234294800-234297200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:234294800-234297200	Enhancers	Lung	lung
36	chr2:234295000-234296800	Enhancers	Stomach Mucosa	stomach
37	chr2:234295000-234297200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:234295000-234297200	Enhancers	Placenta	Placenta
39	chr2:234295000-234297800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:234295200-234298000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:234295400-234296800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:234295400-234297000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr2:234295400-234297000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:234295400-234297000	Enhancers	Fetal Intestine Large	intestine
45	chr2:234295400-234297000	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr2:234295400-234297200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:234295400-234297200	Enhancers	Psoas Muscle	Psoas
48	chr2:234295400-234297200	Enhancers	HUVEC	blood vessel
49	chr2:234295400-234297400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr2:234295400-234297800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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