Variant report

Variant	rs4900353
Chromosome Location	chr14:97353509-97353510
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:97342981..97345508-chr14:97352791..97354634,2	MCF-7	breast:
2	chr14:97347013..97350002-chr14:97352064..97354916,2	K562	blood:
3	chr14:97352755..97355141-chr14:97359581..97361820,2	K562	blood:
4	chr14:97352755..97357017-chr14:97358100..97363870,8	K562	blood:
5	chr14:97349904..97353834-chr14:97354372..97357371,3	K562	blood:
6	chr14:97342578..97345123-chr14:97353355..97355905,2	K562	blood:

Variant related genes	Relation type
ENSG00000100749	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10145383	1.00[CHB][hapmap]
rs10146571	1.00[CHB][hapmap]
rs11160369	0.82[CHB][hapmap]
rs11160377	0.93[ASN][1000 genomes]
rs11627455	0.93[ASN][1000 genomes]
rs11628733	0.82[CHB][hapmap]
rs12101203	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12433112	0.90[CHB][hapmap]
rs12434466	0.80[CHB][hapmap]
rs12586511	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12589919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590169	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12878184	0.90[CHB][hapmap]
rs12881995	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12882038	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12882853	1.00[CHB][hapmap]
rs12887093	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12889255	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12892609	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12893513	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12893711	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894533	0.93[ASN][1000 genomes]
rs12894621	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs12897588	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17191471	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1957135	0.83[CHD][hapmap]
rs2145635	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2145636	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs2180897	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2224442	0.82[CHB][hapmap]
rs2224443	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2230532	0.90[CHB][hapmap]
rs4270096	0.90[CHB][hapmap]
rs4900346	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4900348	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4900350	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs4900351	1.00[CHB][hapmap]
rs4900352	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4905548	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4905549	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4905550	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4905551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4905558	0.90[CHB][hapmap]
rs4905561	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4905562	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4905563	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4905567	0.93[ASN][1000 genomes]
rs7156355	0.90[CHB][hapmap]
rs7158545	0.81[ASN][1000 genomes]
rs723810	0.90[CHB][hapmap]
rs736929	1.00[CHB][hapmap]
rs749279	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs764300	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8013081	0.90[CHB][hapmap]
rs8022152	0.93[ASN][1000 genomes]
rs9323955	0.90[CHB][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044202	chr14:97155291-97683983	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542179	chr14:97155291-97683983	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv948620	chr14:97334444-98133191	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4900353	VRK1	cis	parietal	SCAN
rs4900353	VRK1	cis	cerebellum	SCAN
rs4900353	C14orf177	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:97294000-97362600	Weak transcription	Spleen	Spleen
2	chr14:97299400-97353600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr14:97303400-97371600	Weak transcription	Ovary	ovary
4	chr14:97314800-97355000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:97322200-97354200	Weak transcription	Hela-S3	cervix
6	chr14:97323800-97354600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:97324200-97354200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:97325200-97353800	Weak transcription	Fetal Lung	lung
9	chr14:97325200-97354600	Weak transcription	Thymus	Thymus
10	chr14:97325600-97362000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr14:97331000-97378400	Weak transcription	A549	lung
12	chr14:97337400-97354200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:97338400-97355200	Weak transcription	Psoas Muscle	Psoas
14	chr14:97341000-97354200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr14:97341400-97357400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr14:97342800-97354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr14:97342800-97367000	Weak transcription	NHEK	skin
18	chr14:97343200-97354600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr14:97347000-97354600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr14:97347000-97368200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:97347200-97353800	Weak transcription	Fetal Thymus	thymus
22	chr14:97347200-97354600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr14:97348200-97354200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr14:97348200-97361400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr14:97348600-97356000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:97349000-97354600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr14:97349200-97353600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr14:97349200-97355000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr14:97349200-97359200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr14:97349200-97367200	Weak transcription	Primary B cells from cord blood	blood
31	chr14:97349200-97367600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr14:97349200-97377400	Weak transcription	Primary T cells from cord blood	blood
33	chr14:97349400-97354200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr14:97349400-97354600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:97349400-97354600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr14:97349400-97354800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr14:97349400-97355000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr14:97349400-97356600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:97349400-97359000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr14:97349400-97369200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr14:97353200-97355200	Enhancers	K562	blood
42	chr14:97353400-97353600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:97353400-97354000	Strong transcription	Dnd41	blood
44	chr14:97353400-97355400	Enhancers	GM12878-XiMat	blood
45	chr14:97353400-97356400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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