Variant report

Variant	rs12902794
Chromosome Location	chr15:49867148-49867149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP8B4-1	chr15:49866935-49867306	NONHSAT042381
2	lnc-ATP8B4-1	chr15:49867058-49867306	NONHSAT042382

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10047970	0.83[YRI][hapmap]
rs10048065	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10519229	1.00[CHB][hapmap]
rs10519233	0.84[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs11070699	0.83[YRI][hapmap]
rs11070707	1.00[CEU][hapmap];1.00[CHB][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]
rs11070711	0.82[YRI][hapmap]
rs11632674	0.86[YRI][hapmap]
rs12901416	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];0.99[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]
rs12902107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.99[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]
rs13329455	0.84[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1354918	0.91[EUR][1000 genomes]
rs1354919	1.00[CHB][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1354920	0.85[YRI][hapmap]
rs1395900	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532955	0.86[YRI][hapmap]
rs1546424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1546425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1580996	1.00[CHB][hapmap];0.93[YRI][hapmap]
rs1580997	1.00[CHB][hapmap];0.93[YRI][hapmap]
rs1588127	0.84[CEU][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs16962416	1.00[CHB][hapmap]
rs17402569	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs17480434	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs17481696	0.84[CEU][hapmap]
rs1814711	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1874614	1.00[CHB][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs1874615	0.83[YRI][hapmap]
rs1874616	0.83[YRI][hapmap]
rs1911614	0.86[YRI][hapmap]
rs2202714	0.83[YRI][hapmap]
rs2413947	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2413953	0.83[YRI][hapmap]
rs2413958	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2413963	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs28393768	0.87[EUR][1000 genomes]
rs28408092	0.88[EUR][1000 genomes]
rs28409376	0.86[EUR][1000 genomes]
rs28430272	0.87[EUR][1000 genomes]
rs28465200	0.90[EUR][1000 genomes]
rs28484276	0.88[EUR][1000 genomes]
rs28492008	0.89[EUR][1000 genomes]
rs28568399	0.80[EUR][1000 genomes]
rs28635979	0.89[EUR][1000 genomes]
rs28669217	0.88[EUR][1000 genomes]
rs28671247	0.80[EUR][1000 genomes]
rs28798135	0.84[EUR][1000 genomes]
rs28843724	0.86[EUR][1000 genomes]
rs2899437	1.00[CHB][hapmap]
rs3210227	0.81[EUR][1000 genomes]
rs4303431	0.86[YRI][hapmap]
rs4338740	0.81[TSI][hapmap]
rs4362337	0.93[CEU][hapmap]
rs4396481	1.00[CHB][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs4774539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs4775815	0.86[YRI][hapmap]
rs6493371	0.83[YRI][hapmap]
rs6493376	0.86[YRI][hapmap]
rs7162800	0.83[YRI][hapmap]
rs7166498	0.83[YRI][hapmap]
rs7167041	0.83[YRI][hapmap]
rs7167625	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7170426	0.83[YRI][hapmap]
rs7178101	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs733097	0.86[YRI][hapmap]
rs753857	0.82[LWK][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap]
rs8031680	1.00[CHB][hapmap]
rs8034473	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8035468	0.86[YRI][hapmap]
rs8038373	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8040436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap]
rs8040716	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs967892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs967893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9920574	0.86[EUR][1000 genomes]
rs9972329	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569392	chr15:49789413-49926300	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv3379973	chr15:49823709-49868102	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv1040578	chr15:49841444-49890789	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12902794	SECISBP2L	cis	cerebellum	SCAN
rs12902794	TRPM7	cis	cerebellum	SCAN
rs12902794	DTWD1	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49856200-49897400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:49861600-49868200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:49862600-49869600	Weak transcription	Brain Angular Gyrus	brain
4	chr15:49863400-49874800	Weak transcription	Fetal Kidney	kidney
5	chr15:49863800-49881400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:49864000-49873000	Weak transcription	HSMM	muscle
7	chr15:49864600-49878200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:49864800-49878600	Weak transcription	Primary B cells from cord blood	blood
9	chr15:49864800-49881600	Weak transcription	Brain Substantia Nigra	brain
10	chr15:49865000-49875400	Weak transcription	HSMMtube	muscle
11	chr15:49865000-49880400	Weak transcription	Fetal Lung	lung
12	chr15:49865400-49881400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:49865400-49881800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr15:49865800-49868400	Weak transcription	Gastric	stomach
15	chr15:49865800-49870400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:49866000-49879000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:49866200-49870800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:49866400-49869000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr15:49866400-49875200	Weak transcription	Brain Anterior Caudate	brain
20	chr15:49866800-49868400	Weak transcription	Left Ventricle	heart
21	chr15:49866800-49870200	Weak transcription	Lung	lung
22	chr15:49866800-49871200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:49866800-49872400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:49866800-49872400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:49866800-49873200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:49866800-49873400	Weak transcription	Liver	Liver
27	chr15:49866800-49874800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:49866800-49877200	Weak transcription	Aorta	Aorta
29	chr15:49866800-49881200	Weak transcription	Primary T cells from cord blood	blood
30	chr15:49866800-49881600	Weak transcription	Pancreas	Pancrea
31	chr15:49866800-49897600	Weak transcription	Ovary	ovary

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