Variant report

Variant	rs41287729
Chromosome Location	chr1:86621998-86621999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11161752	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161754	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161755	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161756	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161757	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161758	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11161759	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11578172	0.90[EUR][1000 genomes]
rs11581251	0.90[EUR][1000 genomes]
rs11581326	0.82[EUR][1000 genomes]
rs11583102	0.82[EUR][1000 genomes]
rs11583117	0.82[EUR][1000 genomes]
rs11583120	0.82[EUR][1000 genomes]
rs12068500	0.88[EUR][1000 genomes]
rs12072489	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12072806	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12074275	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12076366	0.86[EUR][1000 genomes]
rs1336052	0.88[EUR][1000 genomes]
rs1336055	0.90[EUR][1000 genomes]
rs1414601	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1507267	0.82[EUR][1000 genomes]
rs1507268	0.90[EUR][1000 genomes]
rs1507276	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1507282	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1507283	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17128866	0.90[EUR][1000 genomes]
rs2039601	0.82[EUR][1000 genomes]
rs2174768	0.90[EUR][1000 genomes]
rs2279948	0.90[EUR][1000 genomes]
rs2892908	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4631724	0.90[EUR][1000 genomes]
rs59694883	0.90[EUR][1000 genomes]
rs6660694	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6668627	0.90[EUR][1000 genomes]
rs6676847	0.82[EUR][1000 genomes]
rs6697869	0.82[EUR][1000 genomes]
rs72716183	0.90[EUR][1000 genomes]
rs72716185	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72716190	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716192	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72716194	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72716202	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72718016	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72718019	0.94[EUR][1000 genomes]
rs72718023	0.90[EUR][1000 genomes]
rs72718033	0.90[EUR][1000 genomes]
rs72718037	0.90[EUR][1000 genomes]
rs7416003	0.86[EUR][1000 genomes]
rs7531445	0.82[EUR][1000 genomes]
rs7536402	0.82[EUR][1000 genomes]
rs954354	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv830481	chr1:86550274-86737290	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2763578	chr1:86584695-86622285	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86619800-86622400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:86620000-86623000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:86620200-86622600	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:86620200-86623000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:86620200-86623000	Active TSS	Right Atrium	heart
6	chr1:86620400-86622000	Enhancers	Gastric	stomach
7	chr1:86620400-86622000	Enhancers	Spleen	Spleen
8	chr1:86620400-86622200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr1:86620400-86622200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:86620400-86622600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:86620400-86622600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr1:86620400-86622600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
13	chr1:86620400-86622800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:86620400-86622800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:86620400-86623000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:86620400-86623000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
17	chr1:86620600-86622400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
18	chr1:86620600-86622800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
19	chr1:86620600-86623000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr1:86620600-86623000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:86620800-86622000	Flanking Active TSS	Right Ventricle	heart
22	chr1:86620800-86622200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr1:86620800-86622400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
24	chr1:86620800-86622800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:86620800-86622800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr1:86620800-86623000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:86620800-86623000	Active TSS	Brain Anterior Caudate	brain
28	chr1:86620800-86623200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:86620800-86623200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr1:86621000-86622000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:86621000-86622600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
32	chr1:86621000-86622600	Active TSS	Aorta	Aorta
33	chr1:86621000-86622600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
34	chr1:86621000-86622600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
35	chr1:86621000-86622800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:86621000-86623000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr1:86621000-86623000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
38	chr1:86621200-86622200	Active TSS	Esophagus	oesophagus
39	chr1:86621200-86622400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:86621200-86622600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:86621200-86622600	Active TSS	Fetal Kidney	kidney
42	chr1:86621200-86622600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr1:86621200-86622800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:86621200-86622800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr1:86621200-86622800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr1:86621200-86622800	Active TSS	Psoas Muscle	Psoas
47	chr1:86621200-86623000	Active TSS	Colon Smooth Muscle	Colon
48	chr1:86621200-86623000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
49	chr1:86621400-86622400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:86621400-86622400	Flanking Bivalent TSS/Enh	NHEK	skin

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