Variant report

Variant	rs790937
Chromosome Location	chr13:50651956-50651957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50651411..50654325-chr13:50705233..50708139,2	K562	blood:
2	chr13:50571255..50572923-chr13:50651167..50653768,2	MCF-7	breast:
3	chr13:50650539..50652612-chr13:50698444..50701026,2	K562	blood:
4	chr13:50569852..50573038-chr13:50651628..50659276,11	K562	blood:
5	chr13:50649792..50652583-chr13:50676207..50678112,2	K562	blood:
6	chr13:50632595..50634463-chr13:50649571..50652516,2	K562	blood:
7	chr13:50651347..50654585-chr13:50679189..50682334,3	K562	blood:
8	chr13:50569462..50575212-chr13:50651363..50657415,15	K562	blood:
9	chr13:50651076..50653449-chr13:50697997..50700597,2	MCF-7	breast:
10	chr13:50648613..50653610-chr13:50653770..50656813,5	MCF-7	breast:
11	chr13:50631606..50635901-chr13:50649525..50652384,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLEU1-2	chr13:50645106-50655642	NONHSAT033808

No data

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000176124	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2066550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472395	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2476389	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490636	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490637	0.82[EUR][1000 genomes]
rs2490638	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2490639	0.82[EUR][1000 genomes]
rs2687933	0.82[EUR][1000 genomes]
rs2687934	0.82[EUR][1000 genomes]
rs2687935	0.82[EUR][1000 genomes]
rs2687936	0.82[EUR][1000 genomes]
rs2812223	0.82[EUR][1000 genomes]
rs34047395	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706609	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs706615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs706617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73489867	0.82[EUR][1000 genomes]
rs790528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790529	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790531	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790928	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790931	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs790934	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790935	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790940	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50578800-50654400	Weak transcription	Esophagus	oesophagus
2	chr13:50586800-50654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:50590200-50653600	Weak transcription	Small Intestine	intestine
4	chr13:50595000-50654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr13:50595800-50654400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:50616000-50653600	Weak transcription	Fetal Kidney	kidney
7	chr13:50617400-50654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:50622600-50653400	Weak transcription	Fetal Brain Male	brain
9	chr13:50622800-50653400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:50624400-50654200	Weak transcription	Pancreas	Pancrea
11	chr13:50625400-50654200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:50626600-50654000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr13:50628400-50652400	Weak transcription	Psoas Muscle	Psoas
14	chr13:50633000-50653600	Weak transcription	Fetal Stomach	stomach
15	chr13:50633400-50652200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr13:50638400-50653400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:50641400-50654200	Weak transcription	Left Ventricle	heart
18	chr13:50641600-50653600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr13:50641800-50654400	Weak transcription	Lung	lung
20	chr13:50642200-50652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr13:50642400-50652200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr13:50642600-50653000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:50642600-50653600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr13:50642600-50654600	Weak transcription	Gastric	stomach
25	chr13:50643000-50652200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr13:50643000-50652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr13:50643000-50653200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:50643200-50653400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:50645200-50652400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr13:50645400-50653000	Enhancers	Primary T cells from cord blood	blood
31	chr13:50645400-50653200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr13:50645600-50652200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr13:50645800-50652200	Weak transcription	Fetal Intestine Large	intestine
34	chr13:50645800-50652600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr13:50646000-50652400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:50646000-50652400	Weak transcription	Brain Anterior Caudate	brain
37	chr13:50646000-50652400	Weak transcription	Fetal Muscle Leg	muscle
38	chr13:50646000-50654200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr13:50646000-50654400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr13:50646200-50654400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr13:50646400-50653000	Weak transcription	Brain Hippocampus Middle	brain
42	chr13:50646600-50653400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr13:50647200-50652200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr13:50648400-50657400	Active TSS	GM12878-XiMat	blood
45	chr13:50649000-50652800	Transcr. at gene 5' and 3'	Dnd41	blood
46	chr13:50649200-50652200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:50649200-50655200	Active TSS	Brain Germinal Matrix	brain
48	chr13:50649600-50652200	Enhancers	HepG2	liver
49	chr13:50649800-50652400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr13:50650000-50652400	Weak transcription	Thymus	Thymus

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