Variant report

Variant	rs1408480
Chromosome Location	chr1:63115497-63115498
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	chr1:63114096..63117270-chr1:63118025..63120771,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493323	1.00[EUR][1000 genomes]
rs10493325	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1168050	1.00[CHB][hapmap]
rs1168121	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023489	1.00[JPT][hapmap]
rs12062275	1.00[CHB][hapmap]
rs12563308	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12563863	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565895	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12566265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17123615	1.00[EUR][1000 genomes]
rs17123688	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17123694	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17123705	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17123712	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123721	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123725	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123743	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123784	0.81[AFR][1000 genomes]
rs2016736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34898550	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36157139	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3737890	1.00[EUR][1000 genomes]
rs55709519	1.00[EUR][1000 genomes]
rs56094630	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56193814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56792530	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57022388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59505425	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59662235	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59816054	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60339595	1.00[EUR][1000 genomes]
rs610248	1.00[EUR][1000 genomes]
rs61308091	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61501887	1.00[EUR][1000 genomes]
rs74076653	1.00[EUR][1000 genomes]
rs74076654	1.00[EUR][1000 genomes]
rs74076668	1.00[EUR][1000 genomes]
rs74076670	1.00[EUR][1000 genomes]
rs74076686	1.00[EUR][1000 genomes]
rs74076689	1.00[EUR][1000 genomes]
rs74076691	1.00[EUR][1000 genomes]
rs74076695	1.00[EUR][1000 genomes]
rs74076699	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74076907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74076909	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74078610	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs74078643	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74078661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817371	chr1:62901935-63129697	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1014376	chr1:62976472-63181359	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63082200-63121000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr1:63082800-63132600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:63083400-63119000	Weak transcription	Fetal Thymus	thymus
4	chr1:63084800-63121000	Weak transcription	Small Intestine	intestine
5	chr1:63088000-63134600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:63096200-63121000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:63096800-63129400	Weak transcription	Esophagus	oesophagus
8	chr1:63098000-63121400	Weak transcription	HUVEC	blood vessel
9	chr1:63099600-63122800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:63099600-63137000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:63107200-63120400	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:63107200-63121000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:63107200-63122600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:63107200-63122600	Weak transcription	Gastric	stomach
15	chr1:63107400-63117600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:63107400-63118600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:63107400-63119400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:63107400-63119800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:63107400-63120800	Weak transcription	Thymus	Thymus
20	chr1:63107400-63121400	Weak transcription	HSMMtube	muscle
21	chr1:63107400-63122400	Weak transcription	Left Ventricle	heart
22	chr1:63107400-63122800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:63107400-63122800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:63107400-63122800	Weak transcription	Lung	lung
25	chr1:63107400-63124800	Weak transcription	Right Ventricle	heart
26	chr1:63107400-63129600	Weak transcription	NHLF	lung
27	chr1:63107400-63132200	Weak transcription	Brain Germinal Matrix	brain
28	chr1:63107400-63151200	Weak transcription	Pancreas	Pancrea
29	chr1:63107600-63147800	Weak transcription	NHEK	skin
30	chr1:63108200-63120200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:63108800-63151200	Weak transcription	Fetal Stomach	stomach
32	chr1:63109000-63124200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:63109000-63130600	Weak transcription	Fetal Intestine Small	intestine
34	chr1:63109000-63147800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:63109200-63117200	Weak transcription	Fetal Kidney	kidney
36	chr1:63109200-63143000	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:63109200-63150200	Weak transcription	Fetal Brain Male	brain
38	chr1:63109400-63118800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:63109400-63120400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:63109400-63121800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:63109600-63121200	Weak transcription	Psoas Muscle	Psoas
42	chr1:63110200-63126200	Weak transcription	NH-A	brain
43	chr1:63110200-63140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:63110400-63116000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:63110600-63120800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:63110800-63117400	Weak transcription	GM12878-XiMat	blood
47	chr1:63111000-63117800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:63111000-63119400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:63111000-63122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:63111000-63124200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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