Variant report

Variant	rs2815368
Chromosome Location	chr1:67500778-67500779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10749766	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10789219	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10889651	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1118392	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs11208971	0.83[EUR][1000 genomes]
rs11208973	0.84[EUR][1000 genomes]
rs11208974	0.84[EUR][1000 genomes]
rs11208979	0.90[JPT][hapmap]
rs1121824	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12041926	0.90[JPT][hapmap]
rs12044278	0.92[JPT][hapmap]
rs12131222	0.92[JPT][hapmap]
rs12137403	0.90[JPT][hapmap]
rs12562761	0.84[EUR][1000 genomes]
rs12742428	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1535365	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570838	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs17497828	0.90[JPT][hapmap]
rs1925408	0.90[JPT][hapmap]
rs1925409	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1925410	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1925411	0.92[JPT][hapmap]
rs1925413	0.92[JPT][hapmap]
rs2025608	0.92[JPT][hapmap]
rs2065000	0.92[JPT][hapmap]
rs2065001	0.90[JPT][hapmap]
rs2065002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2182143	0.90[JPT][hapmap]
rs2755241	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2755242	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2755243	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2755244	0.90[JPT][hapmap]
rs2755245	0.90[JPT][hapmap]
rs2755246	0.90[JPT][hapmap]
rs2755247	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2755250	0.92[JPT][hapmap]
rs2755251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2755254	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2755256	0.82[JPT][hapmap]
rs2755266	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2755270	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2755271	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815349	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815351	0.90[JPT][hapmap]
rs2815355	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815359	0.90[JPT][hapmap]
rs2815360	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815361	0.90[JPT][hapmap]
rs2815362	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815363	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815364	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815365	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815366	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815367	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815370	0.90[JPT][hapmap]
rs2815371	0.90[JPT][hapmap]
rs2815374	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2815375	0.82[ASN][1000 genomes]
rs2985795	0.92[JPT][hapmap]
rs2985797	0.90[JPT][hapmap]
rs2985818	0.90[JPT][hapmap]
rs2985821	0.92[JPT][hapmap]
rs2985822	0.90[JPT][hapmap]
rs2985824	0.90[JPT][hapmap]
rs2985825	0.90[JPT][hapmap]
rs2985826	0.92[JPT][hapmap]
rs3008848	0.90[JPT][hapmap]
rs3008853	0.92[JPT][hapmap]
rs3008854	0.92[JPT][hapmap]
rs3008855	0.90[JPT][hapmap]
rs3008858	0.92[JPT][hapmap]
rs3008871	0.81[JPT][hapmap]
rs3008892	0.90[JPT][hapmap]
rs3736905	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3929738	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4486425	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4581250	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4582760	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4620509	0.92[JPT][hapmap]
rs4655658	0.92[JPT][hapmap]
rs4655660	0.83[EUR][1000 genomes]
rs4655661	0.83[EUR][1000 genomes]
rs4655662	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4655663	0.90[JPT][hapmap]
rs6657065	0.83[EUR][1000 genomes]
rs6673462	0.92[JPT][hapmap]
rs912797	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461751	chr1:67479598-67689036	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv546445	chr1:67479598-67689036	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2815368	MIER1	Cis_1M	lymphoblastoid	RTeQTL
rs2815368	SLC35D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67449400-67501800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:67451200-67506200	Weak transcription	Hela-S3	cervix
3	chr1:67455400-67509400	Weak transcription	Spleen	Spleen
4	chr1:67462400-67508400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:67465200-67502400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:67465200-67506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:67468600-67501800	Weak transcription	Psoas Muscle	Psoas
8	chr1:67470800-67505400	Weak transcription	Gastric	stomach
9	chr1:67471800-67503800	Weak transcription	Brain Substantia Nigra	brain
10	chr1:67472400-67502400	Weak transcription	Fetal Brain Male	brain
11	chr1:67473800-67518000	Weak transcription	A549	lung
12	chr1:67474600-67500800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:67476000-67504600	Weak transcription	Lung	lung
14	chr1:67476000-67508400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:67478000-67508800	Weak transcription	Colonic Mucosa	Colon
16	chr1:67479800-67503200	Weak transcription	K562	blood
17	chr1:67484000-67518400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:67484800-67501800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:67485400-67503600	Weak transcription	Ovary	ovary
20	chr1:67485400-67504000	Weak transcription	Brain Anterior Caudate	brain
21	chr1:67485400-67505800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:67485600-67503000	Weak transcription	Placenta	Placenta
23	chr1:67485800-67503000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:67485800-67504600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:67485800-67506200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:67485800-67507600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:67486000-67501600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:67486000-67509600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:67486200-67516800	Weak transcription	NHEK	skin
30	chr1:67486600-67501800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:67486600-67501800	Weak transcription	Fetal Kidney	kidney
32	chr1:67486600-67502000	Weak transcription	Brain Germinal Matrix	brain
33	chr1:67486800-67501600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr1:67486800-67503200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:67486800-67503800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr1:67486800-67505400	Weak transcription	Left Ventricle	heart
37	chr1:67486800-67509200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:67486800-67515800	Weak transcription	Stomach Mucosa	stomach
39	chr1:67487000-67501600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:67487000-67503000	Weak transcription	NHLF	lung
41	chr1:67487000-67503400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:67487000-67505400	Weak transcription	Esophagus	oesophagus
43	chr1:67487200-67502000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:67487200-67502200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr1:67487200-67502400	Weak transcription	Brain Angular Gyrus	brain
46	chr1:67487200-67503200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:67487200-67504000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:67487200-67505800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:67487600-67504000	Weak transcription	Thymus	Thymus
50	chr1:67487600-67504400	Weak transcription	Fetal Stomach	stomach

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