Variant report

Variant	rs2065002
Chromosome Location	chr1:67487119-67487120
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10749766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10789219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10889651	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1118392	0.92[CEU][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs11208971	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11208973	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11208974	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11208979	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs1121824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041926	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs12044278	0.90[JPT][hapmap]
rs12131222	0.90[JPT][hapmap]
rs12137403	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs12562761	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12742428	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1535365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1570838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17497828	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs1925408	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs1925409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925411	0.90[JPT][hapmap]
rs1925413	0.90[JPT][hapmap]
rs2025608	0.90[JPT][hapmap]
rs2065000	0.90[JPT][hapmap]
rs2065001	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2182143	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2755241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755243	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755244	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2755245	0.90[JPT][hapmap]
rs2755246	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2755247	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2755250	0.90[JPT][hapmap]
rs2755251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2755253	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs2755254	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755266	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2755270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815349	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815351	0.90[JPT][hapmap]
rs2815355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815359	0.88[JPT][hapmap]
rs2815360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815361	0.89[JPT][hapmap]
rs2815362	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815364	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815365	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815366	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815367	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815368	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]
rs2815370	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2815371	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2815374	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2985795	0.90[JPT][hapmap]
rs2985797	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2985818	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2985821	0.90[JPT][hapmap]
rs2985822	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2985824	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2985825	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs2985826	0.90[JPT][hapmap]
rs3008848	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs3008853	0.90[JPT][hapmap]
rs3008854	0.90[JPT][hapmap]
rs3008855	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs3008858	0.90[JPT][hapmap]
rs3008871	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs3008873	0.81[JPT][hapmap]
rs3008892	0.90[JPT][hapmap]
rs3736905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3929738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4486425	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4581250	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4582760	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4620509	0.90[JPT][hapmap]
rs4655658	0.90[JPT][hapmap]
rs4655660	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4655661	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4655662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4655663	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs6657065	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6673462	0.90[JPT][hapmap]
rs912797	0.80[CHD][hapmap];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
rs2065002	MIER1	Cis_1M	lymphoblastoid	RTeQTL
rs2065002	SLC35D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 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	chr1:67455200-67495000	Weak transcription	Small Intestine	intestine
4	chr1:67455400-67509400	Weak transcription	Spleen	Spleen
5	chr1:67462400-67508400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:67465200-67502400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:67465200-67506400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:67468600-67501800	Weak transcription	Psoas Muscle	Psoas
9	chr1:67470800-67505400	Weak transcription	Gastric	stomach
10	chr1:67471800-67503800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:67472400-67502400	Weak transcription	Fetal Brain Male	brain
12	chr1:67473800-67518000	Weak transcription	A549	lung
13	chr1:67474600-67500800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:67476000-67504600	Weak transcription	Lung	lung
15	chr1:67476000-67508400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:67478000-67508800	Weak transcription	Colonic Mucosa	Colon
17	chr1:67479800-67503200	Weak transcription	K562	blood
18	chr1:67480800-67489200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:67481000-67490600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:67481400-67488800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:67482600-67487200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:67482600-67491000	Strong transcription	Primary T cells from cord blood	blood
23	chr1:67482600-67498800	Strong transcription	Fetal Intestine Large	intestine
24	chr1:67483200-67488000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:67483200-67488200	Strong transcription	Dnd41	blood
26	chr1:67483200-67488600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:67483200-67488800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:67483200-67489000	Strong transcription	Primary B cells from cord blood	blood
29	chr1:67483400-67488400	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:67483800-67487200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:67483800-67487600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:67483800-67488200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:67483800-67488400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:67483800-67488400	Strong transcription	Fetal Thymus	thymus
35	chr1:67483800-67488600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr1:67484000-67487200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:67484000-67487600	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:67484000-67487600	Strong transcription	Thymus	Thymus
39	chr1:67484000-67488200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:67484000-67489000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:67484000-67490800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:67484000-67518400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:67484200-67487200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:67484200-67487200	Strong transcription	Brain Angular Gyrus	brain
45	chr1:67484200-67487200	Enhancers	Colon Smooth Muscle	Colon
46	chr1:67484200-67488400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:67484200-67488800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:67484200-67489200	Strong transcription	Fetal Lung	lung
49	chr1:67484400-67487200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:67484400-67488400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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