Variant report

Variant	rs17350991
Chromosome Location	chr1:174083468-174083469
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174073153..174074943-chr1:174081881..174084232,2	K562	blood:
2	chr1:174082792..174085808-chr1:174127455..174130130,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RC3H1-1	chr1:174083005-174084584	NONHSAT007721

Variant related genes	Relation type
ENSG00000227373	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10798302	0.89[YRI][hapmap]
rs10798309	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs10912728	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912733	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912737	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912740	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912746	0.81[EUR][1000 genomes]
rs10912747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10912750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10912751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs10912753	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10912754	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs11802158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12060460	0.85[CEU][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap]
rs12065785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066504	1.00[JPT][hapmap]
rs12066700	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs12067852	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12072050	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12074107	0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12074276	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs12075630	0.92[ASN][1000 genomes]
rs12076453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12076771	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12079214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079687	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079689	0.81[EUR][1000 genomes]
rs12080977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12081445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12082461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12085311	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12087808	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093691	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417186	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846816	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs17300775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350956	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17353198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1934681	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2103640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2142863	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs2142864	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2860907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2860909	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3086	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233169	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4650950	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650951	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650958	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650959	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4650969	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4650981	0.81[EUR][1000 genomes]
rs4652179	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];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652191	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652193	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652204	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55698100	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56152378	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56158362	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239105	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56338048	0.81[EUR][1000 genomes]
rs56375942	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56404641	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57407575	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59044210	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425277	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs6656491	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665484	0.89[YRI][hapmap]
rs6666588	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6668008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670425	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677660	0.89[YRI][hapmap]
rs6678286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs6685499	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689285	0.89[YRI][hapmap]
rs6692437	0.81[EUR][1000 genomes]
rs6693198	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6694208	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696163	0.89[YRI][hapmap]
rs6697959	0.80[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6700482	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs724888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711443	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72711448	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72711457	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711487	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711492	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72711501	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72713503	0.81[EUR][1000 genomes]
rs72713504	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72713505	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs727912	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7547766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7551605	0.81[EUR][1000 genomes]
rs7553317	0.89[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]

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	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv465661	chr1:174014507-174152688	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv548193	chr1:174014507-174152688	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17350991	MRPS14	cis	parietal	SCAN
rs17350991	RP11-160H22.5	cis	Thyroid	GTEx
rs17350991	RC3H1	cis	parietal	SCAN
rs17350991	MRPS14	Cis_1M	lymphoblastoid	RTeQTL
rs17350991	C1orf105	cis	cerebellum	SCAN
rs17350991	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174081800-174086200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:174082200-174084000	Weak transcription	Ovary	ovary
3	chr1:174082800-174084000	Weak transcription	Fetal Heart	heart
4	chr1:174082800-174084000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:174083400-174083600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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