Variant report

Variant	rs3799967
Chromosome Location	chr6:44798701-44798702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 184 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs1023091	0.84[CHB][hapmap]
rs1028944	0.83[CHB][hapmap]
rs1041333	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10456119	0.82[ASN][1000 genomes]
rs10484627	0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10948183	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10948185	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs10948186	0.93[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10948187	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10948188	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs10948190	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948194	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10948195	0.85[EUR][1000 genomes]
rs10948197	0.94[CHB][hapmap]
rs11967188	0.94[CHB][hapmap]
rs12190136	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12190513	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs12191518	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12192367	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs12196818	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs12198904	0.80[ASN][1000 genomes]
rs12207620	0.81[ASN][1000 genomes]
rs12209076	0.83[ASN][1000 genomes]
rs12214778	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs12525009	0.89[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12526711	0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12528232	0.83[CHB][hapmap]
rs12529522	0.81[JPT][hapmap]
rs12530016	0.81[JPT][hapmap]
rs1293457	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1293467	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1293598	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1293600	0.80[EUR][1000 genomes]
rs13199289	0.83[ASN][1000 genomes]
rs13206526	0.88[JPT][hapmap]
rs13209827	0.84[CHB][hapmap]
rs13213412	0.82[ASN][1000 genomes]
rs13215618	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs13216116	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1329710	0.94[CHB][hapmap]
rs1329715	0.83[CHB][hapmap]
rs1329716	0.93[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1342370	0.95[ASN][1000 genomes]
rs1360195	0.83[CHB][hapmap]
rs1360196	0.85[EUR][1000 genomes]
rs1360197	0.94[CHB][hapmap]
rs1402599	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs1418434	0.95[ASN][1000 genomes]
rs1521355	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1557143	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1576382	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16869119	0.88[JPT][hapmap]
rs16872574	0.80[ASN][1000 genomes]
rs17422760	0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs17424547	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1854547	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1891411	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1891412	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1935551	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1971482	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1980265	0.93[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2038555	0.93[ASN][1000 genomes]
rs2038556	0.95[ASN][1000 genomes]
rs2038557	0.95[ASN][1000 genomes]
rs2040032	0.95[ASN][1000 genomes]
rs2139863	0.88[JPT][hapmap]
rs2145826	0.84[EUR][1000 genomes]
rs227849	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs2396369	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2396370	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2396371	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2396372	0.94[CHB][hapmap]
rs2396373	0.86[CEU][hapmap]
rs2894599	0.80[ASN][1000 genomes]
rs34808716	0.82[ASN][1000 genomes]
rs34817919	0.80[ASN][1000 genomes]
rs35687006	0.83[CHB][hapmap]
rs3778507	0.93[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3799965	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3799968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799971	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3799972	0.88[JPT][hapmap]
rs3799973	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs3799974	0.88[JPT][hapmap]
rs3799976	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799977	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799978	0.88[EUR][1000 genomes]
rs3799979	0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs3799981	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799984	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs3799986	0.94[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs3799987	0.83[CHB][hapmap]
rs3823252	0.88[JPT][hapmap]
rs3846896	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3957281	0.82[ASN][1000 genomes]
rs4512220	0.84[CHB][hapmap]
rs4711798	0.95[ASN][1000 genomes]
rs4711799	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4711803	0.83[ASN][1000 genomes]
rs4711805	0.82[ASN][1000 genomes]
rs4711807	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs4711809	0.94[CHB][hapmap]
rs4714812	0.81[JPT][hapmap]
rs4714819	0.94[ASN][1000 genomes]
rs4714820	0.93[ASN][1000 genomes]
rs4714821	0.92[ASN][1000 genomes]
rs4714822	0.95[ASN][1000 genomes]
rs4714828	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs4714830	0.94[CHB][hapmap]
rs4714834	0.83[CHB][hapmap]
rs472672	0.81[ASN][1000 genomes]
rs494982	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs500773	0.83[ASN][1000 genomes]
rs524492	0.88[JPT][hapmap]
rs538801	0.80[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs542444	0.88[JPT][hapmap]
rs567054	0.82[EUR][1000 genomes]
rs57020561	0.87[EUR][1000 genomes]
rs588848	0.82[ASN][1000 genomes]
rs59881382	0.85[ASN][1000 genomes]
rs608941	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs62438007	0.80[ASN][1000 genomes]
rs636845	0.93[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458415	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66642874	0.80[ASN][1000 genomes]
rs679713	0.80[ASN][1000 genomes]
rs6903576	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6904015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910749	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6919161	0.84[CHB][hapmap]
rs6919485	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6923519	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6925017	0.94[CHB][hapmap]
rs6925467	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs6940547	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71564699	0.82[ASN][1000 genomes]
rs718112	0.82[ASN][1000 genomes]
rs72664274	0.80[ASN][1000 genomes]
rs764396	0.85[ASN][1000 genomes]
rs764397	0.85[ASN][1000 genomes]
rs7742360	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7747642	0.81[ASN][1000 genomes]
rs7749865	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs7754378	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7754698	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7763421	0.87[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs7769218	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7775717	0.94[CHB][hapmap]
rs929614	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296448	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9296450	0.83[CHB][hapmap]
rs9349303	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs9357459	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357464	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9367208	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9367211	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9369512	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9369513	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369514	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369515	0.94[EUR][1000 genomes]
rs9369516	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9369519	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9369523	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs9381359	0.85[CEU][hapmap]
rs9395049	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9395051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9395055	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9463054	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9463055	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9472331	0.82[JPT][hapmap]
rs9472336	0.85[ASN][1000 genomes]
rs9472339	0.85[ASN][1000 genomes]
rs9472360	0.95[ASN][1000 genomes]
rs9472376	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs9472383	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9472403	0.88[EUR][1000 genomes]
rs9472407	0.94[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9472409	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs9472414	0.84[CHB][hapmap]
rs9472416	0.94[CHB][hapmap]
rs9472418	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs976699	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842105	chr6:44783457-44798701	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3799967	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs3799967	SUPT3H	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44791000-44805600	Weak transcription	Ovary	ovary
2	chr6:44791200-44799000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:44792000-44811600	Weak transcription	Pancreas	Pancrea
4	chr6:44796800-44799000	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:44796800-44800200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:44796800-44800200	Enhancers	HSMMtube	muscle
7	chr6:44796800-44800400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:44797000-44798800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:44797000-44800600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:44797200-44800000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:44797400-44798800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:44797400-44799200	Enhancers	Fetal Heart	heart
13	chr6:44797400-44800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:44797600-44799000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:44797600-44799200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:44797800-44798800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:44797800-44799000	Weak transcription	Adipose Nuclei	Adipose
18	chr6:44797800-44799800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr6:44797800-44799800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:44798000-44799000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr6:44798000-44799000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:44798000-44799200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:44798200-44799200	Enhancers	Rectal Smooth Muscle	rectum
24	chr6:44798200-44799600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:44798200-44799600	Enhancers	HSMM	muscle
26	chr6:44798200-44800800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:44798200-44811200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:44798400-44800800	Weak transcription	GM12878-XiMat	blood
29	chr6:44798400-44822800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:44798600-44810600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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