Variant report

Variant	rs2284234
Chromosome Location	chr14:78163119-78163120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:104)

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[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10138747	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10139492	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10142722	0.90[CHB][hapmap]
rs10143249	0.89[ASN][1000 genomes]
rs10143294	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10144448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10146255	0.89[ASN][1000 genomes]
rs1048147	0.90[CHB][hapmap]
rs10483885	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs114763	1.00[CHB][hapmap];1.00[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]
rs12879880	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12885306	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs12887313	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12890728	0.85[CHB][hapmap]
rs12890828	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1477262	0.90[CHB][hapmap]
rs1477263	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1477264	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17106157	0.90[CHB][hapmap]
rs176941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176943	0.90[CHB][hapmap]
rs176946	0.90[CHB][hapmap]
rs176947	0.93[ASN][1000 genomes]
rs176948	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176951	0.90[CHB][hapmap]
rs176954	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176955	0.90[CHB][hapmap]
rs176956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176961	0.97[ASN][1000 genomes]
rs176963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176964	0.90[CHB][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176968	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176969	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176970	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176972	0.96[ASN][1000 genomes]
rs176975	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176976	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs176977	0.93[ASN][1000 genomes]
rs176980	0.90[CHB][hapmap]
rs2080703	0.92[ASN][1000 genomes]
rs2111831	0.81[ASN][1000 genomes]
rs2267756	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][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];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2267763	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267764	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267766	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2277917	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2284233	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299930	0.90[CHB][hapmap]
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];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4899673	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs4899674	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4903638	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];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	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6574399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6574404	0.86[CHB][hapmap]
rs7142390	0.90[CHB][hapmap]
rs7143926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145717	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7148078	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7148126	0.92[ASN][1000 genomes]
rs7150531	0.87[ASN][1000 genomes]
rs7151685	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7154571	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7159310	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7160355	0.92[ASN][1000 genomes]
rs717682	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72210300	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs759713	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs8003691	0.90[CHB][hapmap]
rs8010541	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8011337	0.90[CHB][hapmap]
rs8015645	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs8016447	0.90[CHB][hapmap]
rs8022516	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323649	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs9323650	0.90[CHB][hapmap]
rs9323651	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2284234	ALDH6A1	cis	parietal	SCAN
rs2284234	NEK9	cis	parietal	SCAN
rs2284234	RPS6KL1	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr14:78134400-78163400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:78138000-78171800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr14:78140400-78172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:78140600-78173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:78148400-78164400	Weak transcription	Psoas Muscle	Psoas
7	chr14:78149200-78163800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:78149200-78171400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr14:78149800-78164200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr14:78150200-78163800	Strong transcription	Fetal Muscle Leg	muscle
11	chr14:78150400-78172200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr14:78152200-78164200	Strong transcription	Liver	Liver
13	chr14:78152200-78164600	Strong transcription	Adipose Nuclei	Adipose
14	chr14:78152400-78171200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr14:78152600-78172200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:78152800-78165400	Strong transcription	Placenta	Placenta
17	chr14:78152800-78171400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr14:78153400-78171200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr14:78153400-78171400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr14:78153400-78172000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr14:78154400-78168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr14:78154400-78172600	Weak transcription	Small Intestine	intestine
23	chr14:78154600-78167200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr14:78155400-78163600	Strong transcription	HSMM	muscle
25	chr14:78155400-78163800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr14:78155600-78163800	Strong transcription	Fetal Brain Female	brain
27	chr14:78155600-78164000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:78155600-78164800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:78155800-78163800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:78155800-78165600	Strong transcription	Primary T cells from cord blood	blood
31	chr14:78156000-78171400	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr14:78156200-78163800	Strong transcription	Fetal Thymus	thymus
33	chr14:78156200-78164000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr14:78156200-78165000	Strong transcription	Primary B cells from cord blood	blood
35	chr14:78156200-78165200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr14:78156200-78165800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr14:78156200-78172000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr14:78156400-78163800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr14:78156400-78164400	Strong transcription	Thymus	Thymus
40	chr14:78156600-78163600	Strong transcription	K562	blood
41	chr14:78156600-78163800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr14:78156600-78171800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr14:78156800-78163800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr14:78156800-78164000	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr14:78156800-78164200	Strong transcription	Fetal Intestine Large	intestine
46	chr14:78156800-78170000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr14:78156800-78171400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr14:78156800-78172400	Strong transcription	Dnd41	blood
49	chr14:78157200-78163800	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr14:78157400-78164800	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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