Variant report

Variant	rs4899673
Chromosome Location	chr14:78166954-78166955
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:78164522..78168276-chr14:78172771..78175451,7	MCF-7	breast:
2	chr14:78166641..78172350-chr14:78172652..78176323,11	MCF-7	breast:
3	chr14:78165706..78168281-chr14:78176436..78178608,3	MCF-7	breast:
4	chr14:78166071..78168043-chr14:78173060..78175157,2	K562	blood:
5	chr14:78166061..78169254-chr14:78169604..78172317,3	K562	blood:
6	chr14:78158386..78160675-chr14:78164018..78166983,2	MCF-7	breast:
7	chr14:78166468..78169145-chr14:78172506..78175642,4	K562	blood:
8	chr14:78148818..78151260-chr14:78165637..78167371,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100601	Chromatin interaction
ENSG00000239272	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1006038	0.90[CHB][hapmap]
rs1006039	0.90[CHB][hapmap]
rs1006040	0.90[CHB][hapmap]
rs1008988	0.95[CHB][hapmap]
rs10134425	0.97[ASN][1000 genomes]
rs10138747	0.89[ASN][1000 genomes]
rs10139492	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10142722	0.90[CHB][hapmap]
rs10143249	0.89[ASN][1000 genomes]
rs10143294	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10144448	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10146255	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1048147	0.90[CHB][hapmap]
rs10483885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs114763	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11621719	0.85[ASN][1000 genomes]
rs11622761	0.85[ASN][1000 genomes]
rs11624118	0.85[ASN][1000 genomes]
rs11628888	0.85[CHB][hapmap]
rs11846215	0.82[ASN][1000 genomes]
rs12587155	0.81[CEU][hapmap]
rs12879880	0.89[ASN][1000 genomes]
rs12880300	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs12885306	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap]
rs12886631	0.88[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs12887313	0.89[ASN][1000 genomes]
rs12890728	0.85[CHB][hapmap]
rs12890828	0.84[ASN][1000 genomes]
rs1477262	0.90[CHB][hapmap]
rs1477263	0.90[ASN][1000 genomes]
rs1477264	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17106157	0.90[CHB][hapmap]
rs176941	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs176943	0.90[CHB][hapmap]
rs176946	0.90[CHB][hapmap]
rs176947	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176948	0.98[ASN][1000 genomes]
rs176951	0.90[CHB][hapmap]
rs176954	0.98[ASN][1000 genomes]
rs176955	0.90[CHB][hapmap]
rs176956	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs176959	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs176961	0.97[ASN][1000 genomes]
rs176963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs176964	0.90[CHB][hapmap];0.97[ASN][1000 genomes]
rs176965	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs176968	0.97[ASN][1000 genomes]
rs176969	0.97[ASN][1000 genomes]
rs176970	0.97[ASN][1000 genomes]
rs176972	0.96[ASN][1000 genomes]
rs176975	0.97[ASN][1000 genomes]
rs176976	0.97[ASN][1000 genomes]
rs176977	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs176980	0.90[CHB][hapmap]
rs2080703	0.92[ASN][1000 genomes]
rs2111831	0.81[ASN][1000 genomes]
rs2267755	0.81[CEU][hapmap]
rs2267756	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs2267759	0.90[CHB][hapmap]
rs2267760	0.90[CHB][hapmap]
rs2267761	0.90[CHB][hapmap]
rs2267762	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs2267763	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267764	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2277917	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2284233	0.98[ASN][1000 genomes]
rs2284234	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2284235	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2299930	0.90[CHB][hapmap]
rs2299931	0.88[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs3759728	0.90[CHB][hapmap]
rs3783980	0.90[CHB][hapmap]
rs3783981	0.92[ASN][1000 genomes]
rs3783982	0.92[ASN][1000 genomes]
rs4632066	0.90[CHB][hapmap]
rs4641655	0.89[ASN][1000 genomes]
rs4899670	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs4899674	0.95[ASN][1000 genomes]
rs4903624	0.84[CEU][hapmap]
rs4903626	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4903638	0.90[ASN][1000 genomes]
rs61992864	0.80[ASN][1000 genomes]
rs61992867	0.83[ASN][1000 genomes]
rs61992868	0.83[ASN][1000 genomes]
rs6574392	0.93[ASN][1000 genomes]
rs6574394	0.93[ASN][1000 genomes]
rs6574399	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs6574404	0.86[CHB][hapmap]
rs7142390	0.90[CHB][hapmap]
rs7143926	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs7145717	0.90[ASN][1000 genomes]
rs7145979	0.85[CEU][hapmap]
rs7148078	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7148126	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7150531	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7151685	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7154571	0.87[ASN][1000 genomes]
rs7160355	0.92[ASN][1000 genomes]
rs717682	0.87[ASN][1000 genomes]
rs72210300	0.82[ASN][1000 genomes]
rs759713	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs8003691	0.90[CHB][hapmap]
rs8010541	0.93[ASN][1000 genomes]
rs8011337	0.90[CHB][hapmap]
rs8015645	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs8016447	0.90[CHB][hapmap]
rs8022516	0.95[ASN][1000 genomes]
rs9323649	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9323650	0.90[CHB][hapmap]
rs9323651	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv520021	chr14:78152921-78208294	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4899673	ALDH6A1	cis	parietal	SCAN
rs4899673	RPS6KL1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78127400-78173200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78138000-78171800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr14:78140400-78172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:78149200-78171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:78150400-78172200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:78152400-78171200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:78152600-78172200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr14:78152800-78171400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr14:78153400-78171200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr14:78153400-78171400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr14:78153400-78172000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr14:78154400-78168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:78154400-78172600	Weak transcription	Small Intestine	intestine
15	chr14:78154600-78167200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:78156000-78171400	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:78156200-78172000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr14:78156600-78171800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr14:78156800-78170000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:78156800-78171400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr14:78156800-78172400	Strong transcription	Dnd41	blood
22	chr14:78158600-78172800	Weak transcription	NHDF-Ad	bronchial
23	chr14:78159000-78167800	Weak transcription	Gastric	stomach
24	chr14:78162000-78169600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:78162600-78168600	Strong transcription	GM12878-XiMat	blood
26	chr14:78162600-78171400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr14:78163400-78169000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr14:78163600-78168200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr14:78163600-78170200	Weak transcription	Fetal Kidney	kidney
30	chr14:78163600-78170600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr14:78163800-78167000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr14:78163800-78167000	Weak transcription	Fetal Brain Female	brain
33	chr14:78163800-78167000	Weak transcription	Fetal Muscle Leg	muscle
34	chr14:78163800-78167200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr14:78163800-78167200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:78163800-78167200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr14:78163800-78167200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr14:78163800-78167200	Weak transcription	Brain Angular Gyrus	brain
39	chr14:78163800-78167200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr14:78163800-78167200	Weak transcription	Fetal Thymus	thymus
41	chr14:78163800-78167200	Weak transcription	Left Ventricle	heart
42	chr14:78163800-78167400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr14:78163800-78167400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr14:78163800-78167600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr14:78163800-78167800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr14:78163800-78168600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr14:78163800-78168800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr14:78163800-78168800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:78163800-78168800	Weak transcription	Brain Substantia Nigra	brain
50	chr14:78163800-78169000	Weak transcription	Esophagus	oesophagus

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