Variant report

Variant	rs838732
Chromosome Location	chr2:234321752-234321753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234316557..234318837-chr2:234319692..234322100,2	MCF-7	breast:
2	chr2:234320676..234323507-chr2:234330970..234332948,2	MCF-7	breast:
3	chr2:234263404..234265699-chr2:234319043..234321996,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1053895	1.00[ASW][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap]
rs2054071	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242100	0.92[ASW][hapmap];0.86[CHB][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs2924815	0.84[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2971868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762592	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4663540	0.91[CEU][hapmap]
rs55865137	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6706384	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6723558	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7422272	0.91[CEU][hapmap];0.91[GIH][hapmap]
rs768811	0.92[ASW][hapmap];0.91[MEX][hapmap]
rs838707	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs838713	0.87[CEU][hapmap];0.85[CHB][hapmap]
rs838714	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs838715	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs838718	0.86[CHD][hapmap]
rs838719	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]
rs838722	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs838730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs838735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs838732	DGKD	Cis_1M	lymphoblastoid	RTeQTL
rs838732	DGKD	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:234297200-234322000	Weak transcription	Hela-S3	cervix
4	chr2:234297200-234322200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:234308400-234322200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:234308800-234328400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:234309400-234322000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:234309600-234322200	Weak transcription	Esophagus	oesophagus
9	chr2:234312600-234327400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:234316600-234322000	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:234317000-234327400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr2:234317200-234327400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:234317600-234322200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:234317600-234322200	Weak transcription	Fetal Stomach	stomach
15	chr2:234317600-234322400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:234317800-234322200	Weak transcription	Ovary	ovary
17	chr2:234317800-234322200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:234317800-234322800	Weak transcription	Gastric	stomach
19	chr2:234317800-234327400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:234318800-234322200	Weak transcription	Aorta	Aorta
21	chr2:234319000-234322800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:234319200-234321800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:234319200-234321800	Weak transcription	Colonic Mucosa	Colon
24	chr2:234319200-234321800	Weak transcription	Small Intestine	intestine
25	chr2:234319200-234322200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:234319200-234322200	Weak transcription	Placenta	Placenta
27	chr2:234319200-234322200	Weak transcription	Lung	lung
28	chr2:234319200-234322200	Weak transcription	Pancreas	Pancrea
29	chr2:234319200-234322600	Weak transcription	Right Atrium	heart
30	chr2:234319200-234322800	Weak transcription	Left Ventricle	heart
31	chr2:234319200-234322800	Weak transcription	Spleen	Spleen
32	chr2:234319200-234326000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr2:234319200-234326400	Weak transcription	Fetal Thymus	thymus
34	chr2:234319200-234326800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr2:234319200-234326800	Weak transcription	Thymus	Thymus
36	chr2:234319400-234322200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:234319600-234322200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:234319600-234322600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:234319600-234322800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:234319600-234322800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:234319600-234322800	Weak transcription	Fetal Intestine Large	intestine
42	chr2:234319800-234322200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:234319800-234322200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:234319800-234322800	Weak transcription	Fetal Intestine Small	intestine
45	chr2:234320200-234322800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:234320200-234323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:234320400-234322000	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:234320400-234322000	Weak transcription	HSMM	muscle
49	chr2:234320400-234322600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr2:234320600-234322000	Strong transcription	Primary B cells from peripheral blood	blood

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