Variant report

Variant	rs838716
Chromosome Location	chr2:234294791-234294792
allele	C/G
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	POLR2A	chr2:234293034-234295804	GM18505	blood:	n/a	n/a
2	TBL1XR1	chr2:234294131-234294849	GM12878	blood:	n/a	n/a
3	STAT5A	chr2:234293658-234294893	GM12878	blood:	n/a	n/a
4	NFATC1	chr2:234294068-234294832	GM12878	blood:	n/a	n/a
5	MEF2A	chr2:234294121-234294823	GM12878	blood:	n/a	chr2:234294560-234294571 chr2:234294558-234294573
6	BHLHE40	chr2:234293990-234294794	GM12878	blood:	n/a	n/a
7	NFIC	chr2:234294026-234295041	GM12878	blood:	n/a	n/a
8	ATF2	chr2:234294141-234294887	GM12878	blood:	n/a	n/a
9	FOXM1	chr2:234294038-234294865	GM12878	blood:	n/a	n/a
10	PML	chr2:234293885-234294970	GM12878	blood:	n/a	n/a
11	RUNX3	chr2:234293504-234295254	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:234293493-234294860	GM12892	blood:	n/a	n/a
13	STAT5A	chr2:234294117-234294803	GM12878	blood:	n/a	n/a
14	CEBPB	chr2:234294017-234294904	GM12878	blood:	n/a	n/a
15	ATF2	chr2:234294022-234294816	GM12878	blood:	n/a	n/a
16	BCLAF1	chr2:234294028-234294943	GM12878	blood:	n/a	n/a
17	MTA3	chr2:234293391-234295254	GM12878	blood:	n/a	n/a
18	FOXM1	chr2:234294063-234294940	GM12878	blood:	n/a	n/a
19	MEF2A	chr2:234294049-234294889	GM12878	blood:	n/a	chr2:234294560-234294571 chr2:234294558-234294573
20	NFATC1	chr2:234294114-234294810	GM12878	blood:	n/a	n/a
21	MTA3	chr2:234294123-234295101	GM12878	blood:	n/a	n/a
22	RUNX3	chr2:234293970-234294917	GM12878	blood:	n/a	n/a
23	TCF12	chr2:234294747-234297191	A549	lung:	n/a	n/a
24	POLR2A	chr2:234293343-234297175	GM12891	blood:	n/a	n/a
25	NFIC	chr2:234293995-234294995	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAG-1	chr2:234294700-234294860	NONHSAT077483

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000243637	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000259793	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1550532	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2924808	0.92[CEU][hapmap]
rs62195072	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs838708	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs838709	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs838716	DGKD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 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	chr2:234265000-234295000	Weak transcription	Osteobl	bone
3	chr2:234265200-234295000	Weak transcription	NH-A	brain
4	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:234274000-234295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:234280400-234294800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:234281800-234296600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:234282400-234298000	Weak transcription	Dnd41	blood
11	chr2:234284800-234295400	Weak transcription	Fetal Intestine Large	intestine
12	chr2:234285000-234295400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:234287400-234294800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:234289000-234307600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:234290200-234294800	Weak transcription	Small Intestine	intestine
16	chr2:234290600-234297000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:234290800-234296800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr2:234291000-234297000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:234291200-234295800	Enhancers	Thymus	Thymus
20	chr2:234292000-234297200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:234292200-234296400	Enhancers	Primary hematopoietic stem cells	blood
22	chr2:234292200-234296600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:234292200-234297200	Enhancers	Fetal Heart	heart
24	chr2:234292200-234297200	Enhancers	Left Ventricle	heart
25	chr2:234292400-234294800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:234292400-234295800	Enhancers	K562	blood
27	chr2:234292400-234296000	Enhancers	Fetal Lung	lung
28	chr2:234292400-234296200	Enhancers	HepG2	liver
29	chr2:234292400-234296800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr2:234292400-234297200	Enhancers	Right Ventricle	heart
31	chr2:234292600-234297000	Enhancers	Fetal Stomach	stomach
32	chr2:234292600-234297000	Enhancers	Fetal Thymus	thymus
33	chr2:234292600-234298400	Enhancers	Fetal Muscle Leg	muscle
34	chr2:234292800-234295800	Enhancers	Duodenum Mucosa	Duodenum
35	chr2:234292800-234296000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:234292800-234296000	Enhancers	HSMMtube	muscle
37	chr2:234292800-234296200	Enhancers	HSMM	muscle
38	chr2:234292800-234296800	Enhancers	Esophagus	oesophagus
39	chr2:234293000-234295600	Enhancers	Fetal Brain Female	brain
40	chr2:234293000-234296000	Enhancers	Brain Substantia Nigra	brain
41	chr2:234293000-234296000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:234293000-234296200	Enhancers	Brain Cingulate Gyrus	brain
43	chr2:234293000-234296200	Enhancers	Brain Germinal Matrix	brain
44	chr2:234293000-234296200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:234293000-234297000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:234293200-234295800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr2:234293200-234296000	Flanking Active TSS	GM12878-XiMat	blood
48	chr2:234293200-234296200	Enhancers	Brain Hippocampus Middle	brain
49	chr2:234293200-234296400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:234293200-234307600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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