Variant report

Variant	rs12885306
Chromosome Location	chr14:78182677-78182678
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78083955..78086533-chr14:78181911..78184710,2	K562	blood:
2	chr14:78182071..78183613-chr14:78187853..78190331,2	K562	blood:
3	chr14:78181397..78184552-chr14:78187259..78190331,4	K562	blood:
4	chr14:78180959..78183091-chr14:78187177..78189093,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1006038	0.90[CHB][hapmap]
rs1006039	0.90[CHB][hapmap]
rs1006040	0.89[CHB][hapmap]
rs1008988	0.95[CHB][hapmap]
rs10139492	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs10142722	0.90[CHB][hapmap]
rs10143294	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10144448	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]
rs1048147	0.90[CHB][hapmap]
rs10483885	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap]
rs114763	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11628888	0.85[CHB][hapmap]
rs12880300	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs12886631	0.84[CEU][hapmap]
rs12890728	0.85[CHB][hapmap]
rs1477262	0.90[CHB][hapmap]
rs1477264	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs17106157	0.90[CHB][hapmap]
rs176941	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs176943	0.90[CHB][hapmap]
rs176946	0.90[CHB][hapmap]
rs176951	0.90[CHB][hapmap]
rs176955	0.90[CHB][hapmap]
rs176956	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs176959	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs176963	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs176964	0.90[CHB][hapmap]
rs176965	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs176980	0.90[CHB][hapmap]
rs2267756	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs2267759	0.90[CHB][hapmap]
rs2267760	0.90[CHB][hapmap]
rs2267761	0.90[CHB][hapmap]
rs2267762	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs2267763	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2267764	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2277917	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2284234	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs2284235	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs2299930	0.90[CHB][hapmap]
rs2299931	0.84[CEU][hapmap]
rs3759728	0.90[CHB][hapmap]
rs3783980	0.90[CHB][hapmap]
rs4632066	0.90[CHB][hapmap]
rs4899670	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap]
rs4899673	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]
rs4903624	0.83[CEU][hapmap]
rs6574399	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs6574404	0.86[CHB][hapmap]
rs7142390	0.90[CHB][hapmap]
rs7143926	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7145979	0.84[CEU][hapmap]
rs7148078	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs7151685	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]
rs759713	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs8003691	0.90[CHB][hapmap]
rs8011337	0.90[CHB][hapmap]
rs8015645	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs8016447	0.90[CHB][hapmap]
rs9323649	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs9323650	0.90[CHB][hapmap]
rs9323651	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
7	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv3344765	chr14:78182376-78182764	Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv1242183	chr14:78182673-78182677	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv2611528	chr14:78182674-78182677	Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12885306	ALDH6A1	cis	parietal	SCAN
rs12885306	RPS6KL1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78176200-78185400	Weak transcription	Fetal Heart	heart
2	chr14:78176200-78206000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr14:78176200-78208400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:78176200-78224000	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr14:78176200-78225400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr14:78176400-78206200	Strong transcription	Fetal Thymus	thymus
7	chr14:78176400-78223400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr14:78176400-78224200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr14:78176600-78187200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr14:78176600-78187200	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr14:78176600-78197400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:78176600-78204600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr14:78176600-78205200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr14:78176600-78205400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:78176600-78205600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr14:78176600-78205600	Strong transcription	Adipose Nuclei	Adipose
17	chr14:78176600-78205800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr14:78176600-78213200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr14:78176600-78223200	Strong transcription	Fetal Muscle Leg	muscle
20	chr14:78176600-78224200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr14:78176800-78183800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr14:78176800-78190200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr14:78176800-78191400	Weak transcription	Fetal Brain Male	brain
24	chr14:78176800-78192800	Strong transcription	Osteobl	bone
25	chr14:78176800-78205200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr14:78176800-78205600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr14:78176800-78205600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr14:78176800-78205600	Strong transcription	Placenta	Placenta
29	chr14:78176800-78205800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr14:78176800-78206200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr14:78176800-78207400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr14:78176800-78208200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:78176800-78210800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:78176800-78221800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr14:78176800-78222200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr14:78177000-78187200	Strong transcription	Thymus	Thymus
37	chr14:78177000-78189200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr14:78177000-78194800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr14:78177000-78204600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr14:78177000-78204600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr14:78177000-78205000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr14:78177000-78205000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr14:78177000-78205200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr14:78177000-78205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr14:78177000-78205600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr14:78177000-78205800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr14:78177000-78206400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr14:78177000-78206400	Strong transcription	Fetal Intestine Large	intestine
49	chr14:78177000-78211000	Weak transcription	Stomach Mucosa	stomach
50	chr14:78177000-78222600	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links