Variant report

Variant	rs6424650
Chromosome Location	chr1:78479687-78479688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1001070	0.88[AMR][1000 genomes]
rs1001103	0.87[AMR][1000 genomes]
rs1001104	0.90[AMR][1000 genomes]
rs10437022	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10873960	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873962	0.80[AMR][1000 genomes]
rs10873963	0.89[AMR][1000 genomes]
rs11162400	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162403	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11162406	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1166697	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1166701	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1166702	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1166704	0.82[AMR][1000 genomes]
rs1166705	0.85[AMR][1000 genomes]
rs1166706	0.85[AMR][1000 genomes]
rs1166707	0.88[AMR][1000 genomes]
rs11805735	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11807240	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12146104	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12405212	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12409561	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12723748	0.82[AMR][1000 genomes]
rs1335481	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1536160	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1555798	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1616949	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17383213	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17387365	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1855704	0.87[AMR][1000 genomes]
rs1970210	0.80[AMR][1000 genomes]
rs1971368	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2136682	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2274257	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2296453	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3767028	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4370803	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4372306	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4631748	0.89[AMR][1000 genomes]
rs4949828	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949829	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs504388	0.83[AMR][1000 genomes]
rs57421725	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424640	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6424660	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6424664	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6424668	0.84[AMR][1000 genomes]
rs661038	0.83[AMR][1000 genomes]
rs664818	0.83[AMR][1000 genomes]
rs6656888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6677890	0.90[AMR][1000 genomes]
rs6686230	0.86[AMR][1000 genomes]
rs684579	0.82[AMR][1000 genomes]
rs750720	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7514007	0.91[AMR][1000 genomes]
rs7538210	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9324166	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9659938	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9661193	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9730688	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv1801396	chr1:78468094-78492221	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78448800-78488200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:78454200-78485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:78470800-78487800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:78471000-78487400	Weak transcription	Lung	lung
5	chr1:78471200-78486400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:78471600-78483000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:78471600-78483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:78471600-78483800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:78471600-78487000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:78471800-78482000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:78472000-78484800	Weak transcription	Colonic Mucosa	Colon
12	chr1:78472000-78487000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:78472200-78484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:78472400-78483200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:78472400-78486800	Weak transcription	Fetal Thymus	thymus
16	chr1:78472600-78479800	Weak transcription	Fetal Stomach	stomach
17	chr1:78472800-78481600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:78472800-78482000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:78472800-78486400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:78473800-78480200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr1:78473800-78487000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:78474000-78480600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:78474000-78483200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:78474000-78486800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:78474000-78486800	Weak transcription	Pancreas	Pancrea
26	chr1:78474200-78480000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:78474200-78480600	Weak transcription	Fetal Lung	lung
28	chr1:78474200-78482600	Weak transcription	NHEK	skin
29	chr1:78474200-78483600	Weak transcription	HMEC	breast
30	chr1:78474200-78484800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:78474200-78486000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:78474200-78486600	Weak transcription	Primary B cells from cord blood	blood
33	chr1:78474200-78486800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:78474400-78480000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:78474400-78486400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:78475200-78484000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:78475200-78495600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:78475600-78480400	Weak transcription	Left Ventricle	heart
39	chr1:78475800-78480400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:78475800-78480600	Weak transcription	Hela-S3	cervix
41	chr1:78475800-78481600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:78475800-78483400	Weak transcription	Dnd41	blood
43	chr1:78475800-78487800	Weak transcription	Psoas Muscle	Psoas
44	chr1:78475800-78491400	Weak transcription	Ovary	ovary
45	chr1:78476200-78484800	Weak transcription	Small Intestine	intestine
46	chr1:78476600-78486000	Weak transcription	Brain Anterior Caudate	brain
47	chr1:78476800-78480600	Weak transcription	NHLF	lung
48	chr1:78476800-78486200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:78476800-78486600	Weak transcription	Brain Substantia Nigra	brain
50	chr1:78477000-78480000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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