Variant report

Variant	rs351377
Chromosome Location	chr1:212425771-212425772
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212423429..212425837-chr1:212429181..212431560,2	K562	blood:
2	chr1:212424523..212427087-chr1:212457087..212458716,2	K562	blood:
3	chr1:212416179..212418074-chr1:212422362..212425881,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10019	1.00[CEU][hapmap]
rs1009622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs11119884	0.91[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11119885	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs11119887	0.86[ASN][1000 genomes]
rs11119904	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12033246	1.00[CEU][hapmap]
rs12035647	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12036130	0.86[EUR][1000 genomes]
rs12402397	0.83[CHB][hapmap]
rs1389369	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs1389371	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1472226	0.83[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs17042034	0.83[EUR][1000 genomes]
rs1774249	0.82[ASW][hapmap];0.96[CEU][hapmap];0.83[TSI][hapmap]
rs1967117	0.80[ASN][1000 genomes]
rs1992643	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2001234	0.82[ASN][1000 genomes]
rs2012917	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2087946	0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2252044	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs2516331	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2589474	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2884512	0.80[ASN][1000 genomes]
rs3099112	1.00[CEU][hapmap]
rs351373	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351378	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351379	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351380	0.82[EUR][1000 genomes]
rs351386	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351393	1.00[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs351398	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs351401	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs351407	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351408	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs351417	0.86[EUR][1000 genomes]
rs351419	0.90[EUR][1000 genomes]
rs3767861	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs3767862	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs4362041	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs4951582	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951583	0.88[GIH][hapmap]
rs4951589	1.00[CEU][hapmap]
rs6540731	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs6540732	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs6540733	0.83[CHB][hapmap]
rs6657900	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs6668866	0.91[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6679796	0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7415843	1.00[CEU][hapmap]
rs7519168	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs7519959	1.00[CEU][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs7544225	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867584	0.81[ASN][1000 genomes]
rs903120	0.80[ASN][1000 genomes]
rs903121	0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs951623	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs351377	SLC30A1	cis	cerebellum	SCAN
rs351377	CD34	cis	cerebellum	SCAN
rs351377	LGTN	cis	cerebellum	SCAN
rs351377	SYT14	cis	cerebellum	SCAN
rs351377	TMEM206	cis	cerebellum	SCAN
rs351377	TMEM206	cis	Esophagus Mucosa	GTEx
rs351377	TMEM206	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212416600-212430000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:212418200-212428400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:212421600-212428400	Weak transcription	Right Ventricle	heart
4	chr1:212421800-212427600	Weak transcription	Liver	Liver
5	chr1:212423000-212425800	Weak transcription	HepG2	liver
6	chr1:212423600-212431200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr1:212424000-212427400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr1:212424200-212428200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:212424200-212428600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:212424200-212429000	Weak transcription	Stomach Mucosa	stomach
11	chr1:212424400-212425800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:212424400-212425800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr1:212424400-212427400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr1:212424400-212430800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:212424400-212431200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:212424600-212431000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:212425000-212427600	Enhancers	Primary T cells from cord blood	blood
18	chr1:212425000-212428200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:212425000-212428200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:212425200-212425800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:212425200-212427600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:212425200-212428200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:212425400-212427600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr1:212425600-212425800	Enhancers	Primary B cells from cord blood	blood
25	chr1:212425600-212428000	Enhancers	Primary neutrophils fromperipheralblood	blood

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