Variant report

Variant	rs1406899
Chromosome Location	chr6:109816305-109816306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10457192	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10457195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10457203	0.83[EUR][1000 genomes]
rs1046943	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1048203	0.86[CHB][hapmap]
rs10499053	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs1074765	0.88[CEU][hapmap]
rs1074766	0.88[CEU][hapmap]
rs10782162	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs10782163	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10872034	0.95[ASN][1000 genomes]
rs11153174	0.86[CHB][hapmap]
rs11153175	0.86[CHB][hapmap]
rs11153183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153188	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11153213	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs11251	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs11752791	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11754340	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11754455	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]
rs11755641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967108	0.86[CHB][hapmap]
rs12190920	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs12190996	0.84[ASN][1000 genomes]
rs12191353	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12192268	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs12192776	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12192847	0.85[ASN][1000 genomes]
rs12193719	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12194061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12194157	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195904	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12197114	0.86[CHB][hapmap]
rs12197180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197838	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12197950	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12198938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199154	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]
rs12205140	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12205485	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208018	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208933	0.95[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs12209691	0.85[ASN][1000 genomes]
rs12210706	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12212476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214639	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12524639	0.86[CHB][hapmap]
rs12528781	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12528822	0.82[CHB][hapmap]
rs12529733	0.84[CEU][hapmap]
rs13191066	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13199109	0.82[EUR][1000 genomes]
rs13199135	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13201430	0.96[CEU][hapmap]
rs13201947	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13201951	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13203587	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204102	0.82[ASN][1000 genomes]
rs13204500	0.82[ASN][1000 genomes]
rs1321328	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs13220915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358998	0.86[CHB][hapmap]
rs1476387	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1476388	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546980	0.84[ASN][1000 genomes]
rs17070591	0.88[CEU][hapmap]
rs1923725	0.86[CHB][hapmap]
rs1960325	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1980591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1998811	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024850	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]
rs2024852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024853	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[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]
rs2148089	0.80[ASN][1000 genomes]
rs2208209	0.86[ASN][1000 genomes]
rs2236084	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2236582	0.86[CHB][hapmap]
rs2275650	0.82[CHB][hapmap]
rs2277113	0.88[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2277114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357124	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2884037	0.88[CEU][hapmap]
rs35146243	0.83[EUR][1000 genomes]
rs36131450	0.81[ASN][1000 genomes]
rs3734652	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs3757234	0.86[CHB][hapmap]
rs3757235	0.88[CEU][hapmap]
rs3778474	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs3778477	0.85[ASN][1000 genomes]
rs3778478	0.83[EUR][1000 genomes]
rs3799842	0.84[CEU][hapmap]
rs3807005	0.85[ASN][1000 genomes]
rs3899233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4490694	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4945833	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4946967	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs6568592	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68042406	0.95[ASN][1000 genomes]
rs6906216	0.97[ASN][1000 genomes]
rs6911700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6914498	0.95[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs6916579	0.94[ASN][1000 genomes]
rs6920292	0.88[ASN][1000 genomes]
rs6920372	0.88[CEU][hapmap]
rs6926096	0.97[ASN][1000 genomes]
rs6939548	0.83[EUR][1000 genomes]
rs71541003	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs729888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs730089	0.88[CEU][hapmap]
rs7341297	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs736830	0.88[CEU][hapmap]
rs749517	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs752262	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs7748669	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs7754650	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs7755941	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767525	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7768973	0.88[CEU][hapmap]
rs7773095	0.86[CHB][hapmap]
rs7773950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910730	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs9480947	0.88[CEU][hapmap]
rs9480948	0.86[CHB][hapmap]
rs9480956	0.88[CEU][hapmap]
rs9480957	0.86[CHB][hapmap]
rs9487070	0.88[CEU][hapmap]
rs9487100	0.86[CHB][hapmap]
rs9487103	0.87[CEU][hapmap]
rs971434	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs974034	0.88[CEU][hapmap]
rs9791241	0.88[CEU][hapmap];0.83[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1406899	SMPD2	cis	Whole Blood	GTEx
rs1406899	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs1406899	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs1406899	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs1406899	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109805000-109817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:109812000-109816800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr6:109812800-109816800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:109812800-109819000	Weak transcription	Fetal Kidney	kidney
5	chr6:109813400-109816800	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:109813400-109817000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:109813400-109817000	Weak transcription	Primary T cells from cord blood	blood
8	chr6:109813400-109817400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:109813400-109817400	Weak transcription	Placenta	Placenta
10	chr6:109813400-109817400	Weak transcription	HSMMtube	muscle
11	chr6:109813400-109818000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:109813400-109821200	Weak transcription	Thymus	Thymus
13	chr6:109813400-109823000	Weak transcription	HSMM	muscle
14	chr6:109813600-109817400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:109814600-109816400	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr6:109814600-109816600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr6:109814600-109817800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:109814800-109816400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:109815800-109817600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:109815800-109837200	Weak transcription	Primary B cells from cord blood	blood
21	chr6:109816000-109816400	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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