Variant report

Variant	rs838719
Chromosome Location	chr2:234297156-234297157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234164498..234166264-chr2:234297088..234298835,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SAG-1	chr2:234296903-234297631	NONHSAT077483

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2242100	0.88[MEX][hapmap]
rs2971868	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap]
rs34339006	0.84[EUR][1000 genomes]
rs4663540	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs7422272	0.88[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs838707	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs838710	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs838713	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs838714	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838715	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838718	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs838720	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs838722	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs838730	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs838731	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs838732	0.87[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs838733	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs838734	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs838735	0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][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
rs838719	DGKD	Cis_1M	lymphoblastoid	RTeQTL
rs838719	SP100	cis	parietal	SCAN
rs838719	DGKD	cis	cerebellum	SCAN

Chromatin state (count:117 , 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	chr2:234292000-234297200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:234292200-234297200	Enhancers	Fetal Heart	heart
9	chr2:234292200-234297200	Enhancers	Left Ventricle	heart
10	chr2:234292400-234297200	Enhancers	Right Ventricle	heart
11	chr2:234292600-234298400	Enhancers	Fetal Muscle Leg	muscle
12	chr2:234293200-234307600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:234293400-234297200	Enhancers	Brain Angular Gyrus	brain
14	chr2:234293400-234297200	Enhancers	Right Atrium	heart
15	chr2:234293600-234297200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:234293800-234308000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:234293800-234308000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:234294000-234297200	Enhancers	Fetal Brain Male	brain
19	chr2:234294200-234306600	Weak transcription	HMEC	breast
20	chr2:234294600-234297200	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr2:234294600-234298200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:234294600-234318800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr2:234294800-234297200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:234294800-234297200	Enhancers	Lung	lung
25	chr2:234295000-234297200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:234295000-234297200	Enhancers	Placenta	Placenta
27	chr2:234295000-234297800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:234295200-234298000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:234295400-234297200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:234295400-234297200	Enhancers	Psoas Muscle	Psoas
31	chr2:234295400-234297200	Enhancers	HUVEC	blood vessel
32	chr2:234295400-234297400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr2:234295400-234297800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr2:234295400-234300000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:234295400-234305200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:234295400-234313000	Weak transcription	Small Intestine	intestine
37	chr2:234295600-234297200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:234295600-234298600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:234295600-234307600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:234295800-234297200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:234295800-234297800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:234295800-234298600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:234295800-234303400	Weak transcription	Thymus	Thymus
44	chr2:234295800-234308000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:234295800-234318200	Weak transcription	K562	blood
46	chr2:234296000-234297200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:234296000-234297200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:234296000-234297200	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr2:234296000-234297200	Enhancers	Fetal Kidney	kidney
50	chr2:234296000-234297200	Flanking Active TSS	Fetal Lung	lung

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