Variant report

Variant	rs3753563
Chromosome Location	chr1:174923346-174923347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174923198..174925384-chr1:174966768..174969238,3	K562	blood:
2	chr1:174922181..174924698-chr1:174966768..174969386,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS14-2	chr1:174923294-174923398	ENSG00000229531.1

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1046439	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes]
rs1653626	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1653627	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1653632	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1754351	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1754355	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs1793297	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1801791	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes]
rs1984418	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes]
rs2105949	0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap]
rs2187562	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs2187939	0.84[AFR][1000 genomes]
rs2285208	0.84[AFR][1000 genomes]
rs2285210	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap]
rs2987869	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs2987874	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs3018410	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs3118980	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3133270	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4233195	1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs4651238	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[MKK][hapmap];0.81[ASN][1000 genomes]
rs6425305	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap]
rs6425309	0.81[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.88[TSI][hapmap]
rs6425310	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap]
rs6665216	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[MKK][hapmap]
rs6669560	0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap]
rs66700013	0.81[ASN][1000 genomes]
rs7538588	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap]
rs9804056	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs989423	1.00[CHB][hapmap];0.86[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	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1794782	chr1:174900761-174925112	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3753563	TNR	cis	cerebellum	SCAN
rs3753563	TNFSF18	cis	cerebellum	SCAN
rs3753563	MRPS14	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
3	chr1:174908000-174926600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:174908000-174932400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:174908200-174924200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:174908600-174927400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:174908800-174932200	Weak transcription	Primary T cells from cord blood	blood
8	chr1:174910400-174932400	Weak transcription	HSMMtube	muscle
9	chr1:174910800-174925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:174912200-174925400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:174912400-174923800	Weak transcription	Gastric	stomach
13	chr1:174912600-174923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:174912600-174934800	Weak transcription	Left Ventricle	heart
15	chr1:174914800-174932800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:174918600-174923800	Weak transcription	HUVEC	blood vessel
17	chr1:174919200-174926600	Enhancers	Fetal Intestine Large	intestine
18	chr1:174920800-174926200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:174921200-174924400	Enhancers	HepG2	liver
20	chr1:174921200-174924600	Enhancers	Liver	Liver
21	chr1:174921200-174925200	Enhancers	Fetal Intestine Small	intestine
22	chr1:174921400-174925000	Enhancers	Placenta	Placenta
23	chr1:174921800-174924600	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:174921800-174925000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:174922000-174924600	Enhancers	K562	blood
26	chr1:174922000-174925000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:174922200-174923800	Weak transcription	Small Intestine	intestine
28	chr1:174922200-174924000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:174922200-174926600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:174922400-174923400	Enhancers	Fetal Kidney	kidney
31	chr1:174922400-174923800	Enhancers	Primary B cells from cord blood	blood
32	chr1:174922400-174924000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:174922400-174924200	Flanking Active TSS	GM12878-XiMat	blood
34	chr1:174922400-174924400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:174922400-174924400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:174922400-174924400	Enhancers	Fetal Lung	lung
37	chr1:174922400-174924800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:174922400-174924800	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:174922400-174925400	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr1:174922600-174923800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:174922600-174924000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:174922600-174924400	Enhancers	Brain Anterior Caudate	brain
43	chr1:174922600-174924600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr1:174922600-174924600	Enhancers	Brain Substantia Nigra	brain
45	chr1:174922600-174924600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr1:174922600-174924800	Enhancers	Brain Hippocampus Middle	brain
47	chr1:174922600-174925000	Enhancers	Brain Angular Gyrus	brain
48	chr1:174922800-174923800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:174922800-174923800	Weak transcription	Stomach Mucosa	stomach
50	chr1:174922800-174924000	Enhancers	Fetal Muscle Leg	muscle

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