Variant report

Variant	rs1339348
Chromosome Location	chr1:216988982-216988983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1030846	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12745662	0.85[CEU][hapmap]
rs1339337	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1339338	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1339356	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1538526	0.81[CEU][hapmap]
rs1832532	0.87[AMR][1000 genomes]
rs2032028	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2118151	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2576234	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2576235	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2576236	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2576238	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2789716	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2789720	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2813671	0.86[AMR][1000 genomes]
rs2813674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4575149	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6604647	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7512365	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7554036	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][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	esv2762163	chr1:216982140-217015625	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216979800-216989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:216983200-216989200	Weak transcription	Gastric	stomach
3	chr1:216985400-216989000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:216985800-216989000	Weak transcription	Fetal Intestine Large	intestine
5	chr1:216986400-216989600	Enhancers	Fetal Muscle Leg	muscle
6	chr1:216987000-216991000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:216987400-216989600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:216987600-216989200	Weak transcription	Psoas Muscle	Psoas
9	chr1:216987600-216989800	Enhancers	Fetal Kidney	kidney
10	chr1:216987600-216992400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:216987800-216989200	Enhancers	Fetal Lung	lung
12	chr1:216988000-216997200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:216988200-216989600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:216988200-216989600	Enhancers	HSMMtube	muscle
15	chr1:216988400-216989000	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:216988400-216989600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:216988400-216989600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:216988400-216989600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:216988400-216989600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:216988400-216989600	Enhancers	Fetal Intestine Small	intestine
21	chr1:216988400-216989600	Enhancers	Fetal Stomach	stomach
22	chr1:216988400-216989800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:216988600-216989000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:216988600-216989000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:216988600-216989000	Flanking Active TSS	Fetal Heart	heart
26	chr1:216988600-216989000	Enhancers	Left Ventricle	heart
27	chr1:216988600-216989000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:216988600-216989200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:216988600-216989200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr1:216988600-216989200	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:216988600-216989400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:216988600-216989400	Enhancers	Right Atrium	heart
33	chr1:216988600-216989600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:216988600-216989600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr1:216988600-216989600	Enhancers	Fetal Brain Female	brain
36	chr1:216988600-216990000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:216988800-216989000	Enhancers	Brain Germinal Matrix	brain
38	chr1:216988800-216989000	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr1:216988800-216989000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr1:216988800-216989200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:216988800-216989200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:216988800-216989200	Active TSS	Brain Angular Gyrus	brain
43	chr1:216988800-216989200	Active TSS	Brain Anterior Caudate	brain
44	chr1:216988800-216989400	Enhancers	H9 Cell Line	embryonic stem cell
45	chr1:216988800-216989400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:216988800-216989400	Active TSS	Brain Substantia Nigra	brain
47	chr1:216988800-216989400	Enhancers	Fetal Brain Male	brain
48	chr1:216988800-216989600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:216988800-216989600	Enhancers	Small Intestine	intestine
50	chr1:216988800-216989600	Enhancers	HSMM	muscle

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