Variant report

Variant	rs10873961
Chromosome Location	chr1:78484414-78484415
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	chr1:78482811..78485381-chr1:78578750..78581100,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1039863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10735751	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10873962	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10873963	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11162401	0.86[ASN][1000 genomes]
rs1166696	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1166699	0.84[ASN][1000 genomes]
rs1166700	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11805942	0.86[ASN][1000 genomes]
rs11806130	0.88[ASN][1000 genomes]
rs11811805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1510244	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17101101	0.86[ASN][1000 genomes]
rs1749911	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1749913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1780044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1780045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1780047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1780048	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1780052	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2296452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3736909	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3767024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3767025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3790586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4083559	0.83[ASN][1000 genomes]
rs4107671	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4483454	0.84[ASN][1000 genomes]
rs4543852	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4631748	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs4949823	0.81[CHB][hapmap]
rs6424648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6424653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6604878	0.81[CHB][hapmap]
rs6675105	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6680447	0.91[ASN][1000 genomes]
rs6699513	0.82[ASN][1000 genomes]
rs6702465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72685363	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72685364	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72685368	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7520255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7523874	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7524504	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7547599	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9661687	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9662129	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9729146	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[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:76 , 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	chr1:78471600-78487000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:78472000-78484800	Weak transcription	Colonic Mucosa	Colon
8	chr1:78472000-78487000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:78472400-78486800	Weak transcription	Fetal Thymus	thymus
10	chr1:78472800-78486400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:78473800-78487000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:78474000-78486800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:78474000-78486800	Weak transcription	Pancreas	Pancrea
14	chr1:78474200-78484800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:78474200-78486000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:78474200-78486600	Weak transcription	Primary B cells from cord blood	blood
17	chr1:78474200-78486800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:78474400-78486400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:78475200-78495600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:78475800-78487800	Weak transcription	Psoas Muscle	Psoas
21	chr1:78475800-78491400	Weak transcription	Ovary	ovary
22	chr1:78476200-78484800	Weak transcription	Small Intestine	intestine
23	chr1:78476600-78486000	Weak transcription	Brain Anterior Caudate	brain
24	chr1:78476800-78486200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:78476800-78486600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:78477000-78488400	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:78477400-78494000	Weak transcription	Aorta	Aorta
28	chr1:78478400-78485000	Strong transcription	Osteobl	bone
29	chr1:78478600-78485000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:78478600-78485400	Strong transcription	NH-A	brain
31	chr1:78478600-78485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:78478800-78484800	Strong transcription	Liver	Liver
33	chr1:78478800-78485200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:78479200-78487400	Weak transcription	Brain Angular Gyrus	brain
35	chr1:78479400-78486000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:78479400-78493800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:78480600-78487000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:78480800-78485400	Weak transcription	Fetal Stomach	stomach
39	chr1:78480800-78486400	Strong transcription	HSMM	muscle
40	chr1:78481000-78484600	Weak transcription	Right Ventricle	heart
41	chr1:78481000-78485000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:78481000-78485000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:78481000-78486200	Weak transcription	Fetal Intestine Large	intestine
44	chr1:78481000-78486200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:78481000-78486600	Weak transcription	NHLF	lung
46	chr1:78481000-78487600	Weak transcription	Hela-S3	cervix
47	chr1:78481000-78490800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:78481000-78492000	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:78481800-78486600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:78482000-78484600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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