Variant report

Variant	rs17518147
Chromosome Location	chr1:169429035-169429036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC19A2-1	chr1:169429035-169429102	ENSG00000234437.1
2	lnc-SLC19A2-1	chr1:169429035-169429102	ENSG00000234437.1

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1011638	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10489190	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10489417	1.00[AFR][1000 genomes]
rs10494477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10494478	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10800429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10800431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10800432	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10800433	1.00[AFR][1000 genomes]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes]
rs10919127	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes]
rs10919144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10919147	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes]
rs10919149	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919150	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919153	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919158	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919162	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919165	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919172	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022617	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022768	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025397	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025721	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025910	1.00[ASW][hapmap]
rs12028208	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029800	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12030541	1.00[AFR][1000 genomes]
rs12030810	1.00[AFR][1000 genomes]
rs12031371	1.00[AFR][1000 genomes]
rs12036426	1.00[AFR][1000 genomes]
rs12037926	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12042082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12042990	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12044982	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12045803	1.00[AFR][1000 genomes]
rs12048188	1.00[AFR][1000 genomes]
rs12401962	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12402774	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405185	1.00[AFR][1000 genomes]
rs12405725	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs12410387	1.00[AFR][1000 genomes]
rs12567342	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs1517742	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517746	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345426	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes]
rs17345531	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17349677	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17576927	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894691	1.00[ASW][hapmap]
rs1894703	1.00[ASW][hapmap]
rs1949426	0.93[ASN][1000 genomes]
rs2001156	1.00[AFR][1000 genomes]
rs2092083	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766100	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766101	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4497270	1.00[AFR][1000 genomes]
rs4562680	1.00[AFR][1000 genomes]
rs6013	1.00[ASW][hapmap]
rs6018	1.00[ASW][hapmap]
rs6027	1.00[ASW][hapmap]
rs72704035	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72706084	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7413522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7414819	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7522565	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7528142	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7546361	1.00[ASN][1000 genomes]
rs7554853	0.93[ASN][1000 genomes]
rs7556463	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes]
rs9332629	1.00[ASW][hapmap]
rs9332661	1.00[ASW][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17518147	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs17518147	MYOC	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169418600-169429200	Weak transcription	Stomach Mucosa	stomach
2	chr1:169425400-169429800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:169426200-169429400	Weak transcription	Fetal Thymus	thymus
4	chr1:169426600-169429600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:169428800-169429200	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr1:169428800-169429400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:169428800-169429400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:169428800-169429600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:169429000-169429200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:169429000-169429200	Enhancers	Primary T cells from cord blood	blood
11	chr1:169429000-169429200	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:169429000-169429200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:169429000-169429200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:169429000-169429400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr1:169429000-169429400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:169429000-169429400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:169429000-169429800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links