Variant report

Variant	rs909628
Chromosome Location	chr1:169660665-169660666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169658516..169660936-chr1:169662078..169664299,2	K562	blood:

Extended variants
information (count: 134 )
Associated
traits (count: 24 )

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

rs_ID	r²[population]
rs1046058	0.83[CEU][hapmap]
rs10489173	0.83[CEU][hapmap];1.00[MKK][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]
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]
rs12122767	1.00[MKK][hapmap]
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]
rs12130372	1.00[MKK][hapmap]
rs12130784	0.82[AMR][1000 genomes]
rs12132222	0.83[CEU][hapmap]
rs12132384	0.83[CEU][hapmap];1.00[MKK][hapmap]
rs12132633	1.00[CEU][hapmap]
rs12133074	0.83[CEU][hapmap];1.00[MKK][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];1.00[MKK][hapmap]
rs12135642	0.83[CEU][hapmap]
rs12135726	0.83[CEU][hapmap];1.00[MKK][hapmap]
rs12135973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12136425	0.83[CEU][hapmap];1.00[MKK][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];1.00[MKK][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];1.00[MKK][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];1.00[MKK][hapmap]
rs17543730	0.83[CEU][hapmap]
rs17544586	0.83[CEU][hapmap]
rs17593568	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs17601631	0.83[CEU][hapmap];1.00[MKK][hapmap]
rs17602051	0.83[CEU][hapmap]
rs17602072	0.83[CEU][hapmap]
rs17602701	0.83[CEU][hapmap];1.00[MKK][hapmap]
rs17603570	0.82[CEU][hapmap]
rs17603666	0.83[CEU][hapmap];1.00[MKK][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];1.00[MKK][hapmap]
rs3766135	0.83[CEU][hapmap]
rs3766141	0.83[CEU][hapmap];1.00[MKK][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]
rs4987363	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]
rs4987375	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4987381	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][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]
rs9645329	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs909628	C1orf112	cis	cerebellum	SCAN
rs909628	KIFAP3	cis	parietal	SCAN
rs909628	METTL18	cis	Stomach	GTEx
rs909628	METTL18	cis	Muscle Skeletal	GTEx
rs909628	C1orf156	cis	cerebellum	SCAN
rs909628	C1orf156	cis	lymphoblastoid	seeQTL
rs909628	C1orf156	cis	parietal	SCAN
rs909628	METTL18	cis	Esophagus Muscularis	GTEx
rs909628	POGK	cis	cerebellum	SCAN
rs909628	KIFAP3	cis	cerebellum	SCAN
rs909628	METTL18	cis	Artery Aorta	GTEx
rs909628	METTL18	cis	Nerve Tibial	GTEx
rs909628	C1orf156	cis	lesional skin	skin_eQTL
rs909628	METTL18	cis	lung	GTEx
rs909628	METTL18	cis	Thyroid	GTEx
rs909628	METTL18	cis	Heart Left Ventricle	GTEx
rs909628	C1orf156	cis	uninvolved skin	skin_eQTL
rs909628	METTL18	cis	Esophagus Mucosa	GTEx
rs909628	TIPRL	cis	cerebellum	SCAN
rs909628	METTL18	cis	Adipose Subcutaneous	GTEx
rs909628	C1orf156	Cis_1M	lymphoblastoid	RTeQTL
rs909628	ILDR2	cis	cerebellum	SCAN
rs909628	SFT2D2	cis	cerebellum	SCAN
rs909628	METTL18	cis	Artery Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169653200-169671600	Weak transcription	Spleen	Spleen
2	chr1:169656800-169662600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr1:169657000-169661800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:169658400-169666200	Enhancers	Thymus	Thymus
5	chr1:169658600-169661000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr1:169659000-169661600	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr1:169659200-169660800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr1:169659200-169661000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
9	chr1:169659200-169661000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
10	chr1:169659200-169661200	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr1:169659200-169661400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:169659400-169660800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:169659400-169660800	Genic enhancers	Dnd41	blood
14	chr1:169659400-169661200	Genic enhancers	Primary B cells from cord blood	blood
15	chr1:169659400-169661200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:169659600-169660800	Genic enhancers	Primary T cells from cord blood	blood
17	chr1:169659600-169661800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:169659800-169660800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr1:169660000-169660800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr1:169660000-169661200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr1:169660000-169661400	Genic enhancers	Primary hematopoietic stem cells	blood
22	chr1:169660200-169660800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
23	chr1:169660200-169660800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr1:169660200-169660800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:169660200-169660800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:169660200-169661600	Genic enhancers	Monocytes-CD14+_RO01746	blood
27	chr1:169660400-169660800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:169660400-169660800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:169660400-169661200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:169660400-169661800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr1:169660400-169662800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
32	chr1:169660600-169660800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:169660600-169660800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:169660600-169660800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:169660600-169660800	Flanking Active TSS	GM12878-XiMat	blood
36	chr1:169660600-169661200	Genic enhancers	Fetal Thymus	thymus
37	chr1:169660600-169661200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr1:169660600-169663600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr1:169660600-169664000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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