Variant report

Variant	rs10889907
Chromosome Location	chr1:71524753-71524754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:71510894..71514340-chr1:71523075..71528309,6	K562	blood:
2	chr1:71524441..71526375-chr1:71544715..71546592,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000050628	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1005748	0.95[AMR][1000 genomes]
rs1005749	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1008484	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10736414	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10789314	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10889906	1.00[ASN][1000 genomes]
rs12119848	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12122320	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12126880	0.84[EUR][1000 genomes]
rs12131077	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12131515	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142055	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12145536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12145635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1474663	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17542551	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1983587	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2050065	1.00[ASN][1000 genomes]
rs2206344	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2244018	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2247098	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421732	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2744897	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744898	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744899	0.81[AMR][1000 genomes]
rs2744900	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744902	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2744905	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2744906	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744916	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2744918	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2817857	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2817860	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3000466	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493489	0.83[EUR][1000 genomes]
rs496216	0.83[EUR][1000 genomes]
rs508513	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs510414	0.83[EUR][1000 genomes]
rs532693	0.84[EUR][1000 genomes]
rs579558	0.84[EUR][1000 genomes]
rs584532	0.84[EUR][1000 genomes]
rs61777272	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61777274	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61778911	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61778912	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424415	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs651265	0.84[EUR][1000 genomes]
rs653699	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs657265	0.84[EUR][1000 genomes]
rs6670515	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6679003	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6690000	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72671088	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72671095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7529930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs847704	0.84[EUR][1000 genomes]
rs847705	0.84[EUR][1000 genomes]
rs847735	0.81[AMR][1000 genomes]
rs880099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71513600-71533600	Weak transcription	Lung	lung
2	chr1:71514000-71525000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:71514000-71527400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:71514000-71530600	Weak transcription	Ovary	ovary
5	chr1:71514000-71533600	Weak transcription	Pancreas	Pancrea
6	chr1:71514000-71533600	Weak transcription	Right Ventricle	heart
7	chr1:71514200-71533600	Weak transcription	Spleen	Spleen
8	chr1:71515800-71524800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:71515800-71525000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:71515800-71525200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:71515800-71526000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:71515800-71541000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:71517000-71526000	Weak transcription	Thymus	Thymus
14	chr1:71517600-71525000	Weak transcription	NHDF-Ad	bronchial
15	chr1:71519000-71526200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:71519000-71530200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:71519200-71525000	Weak transcription	HUVEC	blood vessel
18	chr1:71519200-71525800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:71519200-71533400	Weak transcription	Fetal Intestine Small	intestine
20	chr1:71519400-71525600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr1:71519400-71528200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:71519600-71528000	Weak transcription	Brain Germinal Matrix	brain
23	chr1:71520000-71536800	Weak transcription	Aorta	Aorta
24	chr1:71520200-71525200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:71520200-71525800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:71520400-71533600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:71520400-71534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:71520600-71524800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:71520600-71526400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:71520600-71527200	Weak transcription	Fetal Kidney	kidney
31	chr1:71520600-71533600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:71520600-71544600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:71520800-71527400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:71521000-71525000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:71521000-71525200	Weak transcription	Fetal Intestine Large	intestine
36	chr1:71521000-71529800	Weak transcription	Brain Angular Gyrus	brain
37	chr1:71521200-71533600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:71521400-71530400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:71521400-71544200	Strong transcription	Adipose Nuclei	Adipose
40	chr1:71521600-71528400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:71521600-71536800	Weak transcription	Stomach Mucosa	stomach
42	chr1:71521800-71525800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:71521800-71525800	Weak transcription	Fetal Brain Male	brain
44	chr1:71521800-71526000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:71521800-71526400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:71521800-71530400	Weak transcription	Small Intestine	intestine
47	chr1:71521800-71544600	Strong transcription	HSMM	muscle
48	chr1:71522000-71526200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:71522000-71528200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr1:71522000-71534400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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