Variant report

Variant	rs821377
Chromosome Location	chr1:86139917-86139918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10747324	1.00[JPT][hapmap]
rs1094360	0.81[ASN][1000 genomes]
rs12037294	0.88[ASN][1000 genomes]
rs12410234	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12758966	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1481200	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17128293	0.81[ASN][1000 genomes]
rs1764287	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1764294	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1764295	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1764296	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1764298	0.98[EUR][1000 genomes]
rs1775985	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1775986	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1775987	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1775992	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1775993	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2014733	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2389973	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2389974	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2785082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2970548	0.88[ASN][1000 genomes]
rs313723	0.81[ASN][1000 genomes]
rs313724	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs313725	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs399547	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs425357	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs429040	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4379699	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs444875	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6686719	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7521240	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs821378	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821380	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821382	0.88[ASN][1000 genomes]
rs821383	0.88[ASN][1000 genomes]
rs821385	0.81[ASN][1000 genomes]
rs821387	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821388	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821390	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821397	0.88[ASN][1000 genomes]
rs821400	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821402	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs821403	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs821404	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs849158	0.88[ASN][1000 genomes]
rs9324152	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9324153	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9432948	0.85[EUR][1000 genomes]
rs9651138	0.81[ASN][1000 genomes]
rs9661608	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9661951	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9701898	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9793547	0.88[EUR][1000 genomes]
rs9793556	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
2	chr1:86103600-86141200	Weak transcription	Thymus	Thymus
3	chr1:86103600-86142200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:86103600-86145400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:86103600-86145600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:86103600-86157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:86103600-86172600	Weak transcription	Gastric	stomach
9	chr1:86106000-86141200	Weak transcription	Lung	lung
10	chr1:86114000-86141200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:86114000-86143600	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:86114400-86142200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
14	chr1:86115200-86146800	Weak transcription	Psoas Muscle	Psoas
15	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:86115400-86141000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:86116400-86143600	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:86116400-86146200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:86116600-86142200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:86116600-86145400	Weak transcription	Fetal Stomach	stomach
21	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
22	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
23	chr1:86119200-86142200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:86119200-86142200	Weak transcription	Placenta	Placenta
25	chr1:86119400-86140600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:86119400-86140800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:86119400-86142200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:86119400-86142200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:86119400-86143400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:86119600-86140600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:86119600-86142200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:86119600-86157800	Weak transcription	Hela-S3	cervix
33	chr1:86119600-86172000	Weak transcription	Colonic Mucosa	Colon
34	chr1:86119800-86171800	Weak transcription	Fetal Brain Male	brain
35	chr1:86120000-86140000	Weak transcription	Left Ventricle	heart
36	chr1:86120000-86140600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:86120000-86141000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:86120000-86142000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:86120000-86142000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:86120200-86144000	Weak transcription	Brain Anterior Caudate	brain
41	chr1:86120200-86146200	Weak transcription	Brain Angular Gyrus	brain
42	chr1:86120600-86140000	Weak transcription	HSMMtube	muscle
43	chr1:86120800-86141000	Weak transcription	NHLF	lung
44	chr1:86120800-86141200	Weak transcription	NHEK	skin
45	chr1:86123200-86141200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:86127600-86140800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:86127600-86142000	Weak transcription	A549	lung
48	chr1:86127600-86146800	Weak transcription	Fetal Kidney	kidney
49	chr1:86128600-86146000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:86129000-86144600	Strong transcription	Monocytes-CD14+_RO01746	blood

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