Variant report

Variant	rs4987302
Chromosome Location	chr1:169674983-169674984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169674141..169677050-chr1:169763005..169764633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1046058	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10489173	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10489174	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10489176	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12116738	0.83[EUR][1000 genomes]
rs12119368	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12119635	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12120647	0.82[AMR][1000 genomes]
rs12121045	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12121313	0.82[AMR][1000 genomes]
rs12121443	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12121606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12121614	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12121681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12122419	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12122582	0.82[AMR][1000 genomes]
rs12122767	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12122776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12122781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12123432	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12123942	0.82[AMR][1000 genomes]
rs12124032	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12125023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12126591	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12127500	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12128695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12128704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12128929	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12129443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12130372	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12130784	0.82[AMR][1000 genomes]
rs12131357	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs12132222	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12132384	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12132633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12133074	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12133642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134837	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12135214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135361	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12135642	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12135726	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12135973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136425	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12137905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs12141317	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12141572	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142093	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12142956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143057	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12143161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12143301	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12144207	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12144683	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12145417	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12145458	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12145504	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12145574	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1569457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs16828222	0.83[CEU][hapmap]
rs17527744	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17529304	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs17529791	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17543370	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17543611	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17543730	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17544586	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs17544823	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs17593568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs17601631	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17602051	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs17602072	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17602701	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17603570	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs17603666	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs1800015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1800016	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1805193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2272919	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2272920	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs3766135	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766141	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766143	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3917388	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917396	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3917410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3917411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917424	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3917448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3917452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3917709	1.00[YRI][hapmap]
rs3917729	1.00[YRI][hapmap]
rs4987267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987284	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4987307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4987308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4987317	1.00[CHB][hapmap];1.00[JPT][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]
rs4987323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4987324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4987326	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987327	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987340	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987343	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987345	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987363	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987375	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4987381	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4987395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs5357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56230202	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57357201	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs909628	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9645329	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1009313	chr1:169661299-169680173	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv872541	chr1:169672360-169695815	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4987302	METTL18	cis	lung	GTEx
rs4987302	METTL18	cis	Heart Left Ventricle	GTEx
rs4987302	C1orf156	cis	uninvolved skin	skin_eQTL
rs4987302	METTL18	cis	Muscle Skeletal	GTEx
rs4987302	METTL18	cis	Artery Tibial	GTEx
rs4987302	METTL18	cis	Adipose Subcutaneous	GTEx
rs4987302	METTL18	cis	Stomach	GTEx
rs4987302	METTL18	cis	Nerve Tibial	GTEx
rs4987302	METTL18	cis	Esophagus Mucosa	GTEx
rs4987302	METTL18	cis	Artery Aorta	GTEx
rs4987302	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs4987302	METTL18	cis	Thyroid	GTEx
rs4987302	METTL18	cis	Esophagus Muscularis	GTEx
rs4987302	C1orf156	cis	lesional skin	skin_eQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169662400-169676000	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr1:169667600-169676800	Genic enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:169668000-169677400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
4	chr1:169670600-169678000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chr1:169671000-169675000	Genic enhancers	Monocytes-CD14+_RO01746	blood
6	chr1:169671200-169679400	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr1:169672600-169677400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
8	chr1:169672600-169678000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:169672800-169676000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:169673200-169676800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
11	chr1:169673200-169678400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
12	chr1:169673400-169676600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
13	chr1:169673800-169675800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:169674000-169675200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:169674000-169675600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:169674000-169675800	Weak transcription	GM12878-XiMat	blood
17	chr1:169674000-169676000	Strong transcription	Fetal Thymus	thymus
18	chr1:169674000-169676000	Weak transcription	Thymus	Thymus
19	chr1:169674000-169676200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:169674200-169675000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:169674400-169675000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:169674400-169675000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:169674400-169675800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:169674400-169678000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
25	chr1:169674600-169675400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:169674800-169675000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:169674800-169675400	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr1:169674800-169675400	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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