Variant report

Variant	rs2139863
Chromosome Location	chr6:44796139-44796140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44794819..44797598-chr6:44800696..44803028,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1023091	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1028944	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10484627	0.83[JPT][hapmap]
rs12525773	0.87[ASN][1000 genomes]
rs12526711	0.83[JPT][hapmap]
rs12526755	0.87[ASN][1000 genomes]
rs12527908	0.91[ASN][1000 genomes]
rs12528232	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs12529522	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12530016	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12661902	0.86[ASN][1000 genomes]
rs12663530	0.88[ASN][1000 genomes]
rs12663798	0.87[ASN][1000 genomes]
rs13199289	0.82[ASN][1000 genomes]
rs13202672	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13206526	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13216967	0.85[ASN][1000 genomes]
rs1329715	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1360195	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs1402599	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1418435	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16869119	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16872574	0.98[ASN][1000 genomes]
rs17422760	0.83[JPT][hapmap]
rs1935549	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227852	1.00[CHB][hapmap]
rs227853	1.00[CHB][hapmap]
rs227857	0.84[ASN][1000 genomes]
rs2894599	0.98[ASN][1000 genomes]
rs34243039	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34286542	0.86[ASN][1000 genomes]
rs34577161	0.86[AMR][1000 genomes]
rs34776198	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34817919	0.98[ASN][1000 genomes]
rs35103634	0.87[ASN][1000 genomes]
rs35687006	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs35704584	0.87[ASN][1000 genomes]
rs35856781	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35908738	0.87[ASN][1000 genomes]
rs36105034	0.86[ASN][1000 genomes]
rs3799965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799966	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799967	0.88[JPT][hapmap]
rs3799969	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799970	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799971	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs3799972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799973	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs3799974	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799976	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3799977	0.83[JPT][hapmap]
rs3799979	0.83[JPT][hapmap]
rs3799984	0.84[JPT][hapmap]
rs3799987	0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs3823252	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3997503	0.86[ASN][1000 genomes]
rs4475320	0.87[ASN][1000 genomes]
rs4512220	0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs4711797	0.85[AMR][1000 genomes]
rs4711809	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs4714812	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes]
rs4714825	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4714827	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714828	0.83[JPT][hapmap]
rs4714829	0.87[ASN][1000 genomes]
rs4714834	0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs524492	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs542444	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs562016	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59945128	0.87[ASN][1000 genomes]
rs609643	0.84[ASN][1000 genomes]
rs609699	0.84[ASN][1000 genomes]
rs66642874	0.98[ASN][1000 genomes]
rs67597621	0.97[ASN][1000 genomes]
rs67911131	0.89[ASN][1000 genomes]
rs6904015	0.89[JPT][hapmap]
rs6904584	0.91[ASN][1000 genomes]
rs6910294	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6919161	0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs720988	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720989	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72664272	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72664273	0.97[ASN][1000 genomes]
rs72664274	0.98[ASN][1000 genomes]
rs7746032	0.86[ASN][1000 genomes]
rs7754378	0.83[JPT][hapmap]
rs7754698	0.87[JPT][hapmap]
rs7769218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296450	0.88[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9367211	0.82[JPT][hapmap]
rs9369514	0.83[JPT][hapmap]
rs9369516	0.83[JPT][hapmap]
rs9395051	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9463017	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9463039	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9463040	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9472331	1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes]
rs9472335	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9472376	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9472407	0.83[JPT][hapmap]
rs9472414	0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs9885796	0.86[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2139863	SUPT3H	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44777400-44796600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:44779600-44796200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:44779600-44796600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:44779600-44796800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:44779600-44796800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:44780000-44798400	Weak transcription	Dnd41	blood
7	chr6:44785200-44796800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:44785800-44796400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:44786200-44797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:44789200-44796800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr6:44790400-44797200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:44791000-44805600	Weak transcription	Ovary	ovary
13	chr6:44791200-44796400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:44791200-44799000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:44792000-44811600	Weak transcription	Pancreas	Pancrea
16	chr6:44792200-44796600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr6:44792400-44796800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:44792600-44796200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:44792800-44796600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:44792800-44796800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:44792800-44797000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:44792800-44797200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:44793400-44797200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:44793400-44798000	Weak transcription	HepG2	liver
25	chr6:44793600-44796600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:44793800-44797400	Weak transcription	Fetal Intestine Large	intestine
27	chr6:44794200-44796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:44794600-44798200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr6:44795000-44796800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:44795200-44796400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:44795600-44798200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:44795800-44798000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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