Variant report

Variant	rs4987363
Chromosome Location	chr1:169663938-169663939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169570098..169571225-chr1:169663167..169664353,5	MCF-7	breast:
2	chr1:169519013..169520404-chr1:169662765..169663989,4	MCF-7	breast:
3	chr1:169555471..169556167-chr1:169663467..169664121,3	MCF-7	breast:
4	chr1:169658516..169660936-chr1:169662078..169664299,2	K562	blood:

Variant related genes	Relation type
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1046058	0.83[CEU][hapmap]
rs10489173	0.83[CEU][hapmap]
rs10489174	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs10489176	0.83[CEU][hapmap]
rs12067152	1.00[YRI][hapmap]
rs12116738	0.85[EUR][1000 genomes]
rs12119368	0.83[CEU][hapmap]
rs12119635	0.83[CEU][hapmap]
rs12120647	0.82[AMR][1000 genomes]
rs12121045	0.83[CEU][hapmap]
rs12121313	0.82[AMR][1000 genomes]
rs12121443	0.83[CEU][hapmap]
rs12121606	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs12121614	0.83[CEU][hapmap]
rs12121681	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12122419	0.83[CEU][hapmap]
rs12122582	0.82[AMR][1000 genomes]
rs12122776	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12122781	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12123432	0.82[CEU][hapmap]
rs12123942	0.82[AMR][1000 genomes]
rs12124032	0.83[CEU][hapmap]
rs12125023	1.00[CEU][hapmap]
rs12126591	0.83[CEU][hapmap]
rs12127500	0.83[CEU][hapmap]
rs12128695	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12128704	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12128929	0.83[CEU][hapmap]
rs12129443	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs12130784	0.82[AMR][1000 genomes]
rs12131357	0.80[CEU][hapmap]
rs12132222	0.83[CEU][hapmap]
rs12132384	0.83[CEU][hapmap]
rs12132633	1.00[CEU][hapmap]
rs12133074	0.83[CEU][hapmap]
rs12133642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12133666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12133892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12134837	0.83[CEU][hapmap]
rs12135214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12135361	0.83[CEU][hapmap]
rs12135642	0.83[CEU][hapmap]
rs12135726	0.83[CEU][hapmap]
rs12135973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12136425	0.83[CEU][hapmap]
rs12137905	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12141317	0.83[CEU][hapmap]
rs12141572	1.00[JPT][hapmap]
rs12142093	0.83[CEU][hapmap]
rs12142956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12142988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12143057	0.83[CEU][hapmap]
rs12143301	0.83[CEU][hapmap]
rs12144207	0.83[CEU][hapmap]
rs12144683	0.83[CEU][hapmap]
rs12145417	0.83[CEU][hapmap]
rs12145458	0.83[CEU][hapmap]
rs12145504	0.82[AMR][1000 genomes]
rs12145574	0.83[CEU][hapmap]
rs1569457	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17527744	0.82[AMR][1000 genomes]
rs17529304	0.83[CEU][hapmap]
rs17529791	0.83[CEU][hapmap]
rs17543370	0.83[CEU][hapmap]
rs17543611	0.83[CEU][hapmap]
rs17543730	0.83[CEU][hapmap]
rs17544586	0.83[CEU][hapmap]
rs17544823	0.83[CEU][hapmap]
rs17593568	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs17601631	0.83[CEU][hapmap]
rs17602051	0.83[CEU][hapmap]
rs17602072	0.83[CEU][hapmap]
rs17602701	0.83[CEU][hapmap]
rs17603570	0.82[CEU][hapmap]
rs17603666	0.83[CEU][hapmap]
rs1800015	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1800016	1.00[ASW][hapmap];0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1800808	1.00[YRI][hapmap]
rs1805193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2272919	0.83[CEU][hapmap]
rs2272920	0.83[CEU][hapmap]
rs3766135	0.83[CEU][hapmap]
rs3766141	0.83[CEU][hapmap]
rs3766143	0.83[CEU][hapmap]
rs3917388	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3917392	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3917396	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917400	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs3917410	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3917411	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917417	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917424	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917425	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917427	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917441	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3917448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3917452	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3917453	1.00[YRI][hapmap]
rs3917675	1.00[YRI][hapmap]
rs3917681	1.00[YRI][hapmap]
rs3917709	1.00[YRI][hapmap]
rs3917724	1.00[JPT][hapmap]
rs3917729	1.00[YRI][hapmap]
rs4987267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987284	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987299	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4987302	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987304	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987307	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987308	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987317	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987323	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987324	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987325	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4987326	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4987327	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4987340	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4987343	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4987345	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4987375	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987381	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4987395	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5357	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5361	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5362	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5367	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56230202	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57357201	0.86[AMR][1000 genomes]
rs909628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9645329	0.83[CEU][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	nsv872539	chr1:169658586-169674590	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs4987363	POGK	cis	cerebellum	SCAN
rs4987363	METTL18	cis	Thyroid	GTEx
rs4987363	METTL18	cis	Adipose Subcutaneous	GTEx
rs4987363	METTL18	cis	Stomach	GTEx
rs4987363	KIFAP3	cis	cerebellum	SCAN
rs4987363	C1orf112	cis	cerebellum	SCAN
rs4987363	METTL18	cis	Esophagus Mucosa	GTEx
rs4987363	METTL18	cis	Artery Tibial	GTEx
rs4987363	C1orf156	cis	lesional skin	skin_eQTL
rs4987363	TIPRL	cis	cerebellum	SCAN
rs4987363	C1orf156	cis	uninvolved skin	skin_eQTL
rs4987363	C1orf156	cis	cerebellum	SCAN
rs4987363	SFT2D2	cis	cerebellum	SCAN
rs4987363	METTL18	cis	Artery Aorta	GTEx
rs4987363	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs4987363	METTL18	cis	Nerve Tibial	GTEx
rs4987363	C1orf156	cis	parietal	SCAN
rs4987363	METTL18	cis	lung	GTEx
rs4987363	METTL18	cis	Heart Left Ventricle	GTEx
rs4987363	METTL18	cis	Muscle Skeletal	GTEx
rs4987363	ILDR2	cis	cerebellum	SCAN
rs4987363	C1orf156	cis	lymphoblastoid	seeQTL
rs4987363	KIFAP3	cis	parietal	SCAN
rs4987363	METTL18	cis	Esophagus Muscularis	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169653200-169671600	Weak transcription	Spleen	Spleen
2	chr1:169658400-169666200	Enhancers	Thymus	Thymus
3	chr1:169660600-169664000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:169660800-169664200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
5	chr1:169660800-169665200	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:169661200-169664000	Enhancers	Fetal Thymus	thymus
7	chr1:169661200-169665400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:169661600-169664000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr1:169662000-169664200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr1:169662000-169665800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:169662000-169667400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:169662400-169664000	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr1:169662400-169664000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr1:169662400-169676000	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr1:169662800-169664000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:169662800-169664200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
17	chr1:169662800-169664800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:169663200-169664400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:169663200-169664400	Enhancers	Brain Hippocampus Middle	brain
20	chr1:169663200-169664800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:169663200-169669000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:169663200-169674000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:169663400-169664000	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
24	chr1:169663600-169664000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:169663600-169665600	Enhancers	GM12878-XiMat	blood
26	chr1:169663800-169664000	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:169663800-169664000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr1:169663800-169664000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:169663800-169664000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:169663800-169664000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:169663800-169664200	Flanking Active TSS	Dnd41	blood
32	chr1:169663800-169664400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr1:169663800-169665800	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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