Variant report

Variant	rs1041604
Chromosome Location	chr1:57038169-57038170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10789030	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12126955	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1777275	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2065553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065555	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2404719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2404983	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4469733	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6588640	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs7545642	0.86[MEX][hapmap]
rs7549799	0.85[AMR][1000 genomes];0.97[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57016000-57038600	Weak transcription	HSMMtube	muscle
2	chr1:57017400-57039400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:57017800-57040800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:57025600-57040000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:57029400-57042200	Weak transcription	Thymus	Thymus
6	chr1:57032000-57038800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:57032200-57040600	Weak transcription	HSMM	muscle
8	chr1:57032400-57042400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:57032800-57038200	Weak transcription	Osteobl	bone
10	chr1:57032800-57039200	Weak transcription	Small Intestine	intestine
11	chr1:57032800-57041000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:57033000-57038200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:57033000-57038800	Weak transcription	Fetal Brain Male	brain
14	chr1:57033800-57039800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:57034200-57038200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:57035200-57039600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:57035200-57039600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr1:57035200-57039600	Enhancers	Fetal Intestine Large	intestine
19	chr1:57035200-57041400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:57035400-57038200	Genic enhancers	Muscle Satellite Cultured Cells	--
21	chr1:57035400-57039400	Enhancers	Brain Substantia Nigra	brain
22	chr1:57035400-57039400	Enhancers	Stomach Mucosa	stomach
23	chr1:57035400-57039600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
24	chr1:57035400-57039800	Enhancers	Brain Angular Gyrus	brain
25	chr1:57035600-57038800	Enhancers	Adipose Nuclei	Adipose
26	chr1:57035600-57038800	Enhancers	HepG2	liver
27	chr1:57035800-57038200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr1:57035800-57038600	Weak transcription	Aorta	Aorta
29	chr1:57035800-57039000	Enhancers	A549	lung
30	chr1:57035800-57039800	Weak transcription	Lung	lung
31	chr1:57036400-57038200	Enhancers	Fetal Muscle Leg	muscle
32	chr1:57036400-57040800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:57036600-57038400	Enhancers	Brain Hippocampus Middle	brain
34	chr1:57036600-57039000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:57036600-57039000	Genic enhancers	NHLF	lung
36	chr1:57036600-57039400	Enhancers	Placenta	Placenta
37	chr1:57036600-57039600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:57036600-57039800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:57036600-57040600	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:57036600-57040600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr1:57036800-57038200	Enhancers	Colon Smooth Muscle	Colon
42	chr1:57036800-57038200	Enhancers	Esophagus	oesophagus
43	chr1:57036800-57038200	Enhancers	Left Ventricle	heart
44	chr1:57036800-57038200	Enhancers	Pancreas	Pancrea
45	chr1:57036800-57038400	Enhancers	Psoas Muscle	Psoas
46	chr1:57036800-57038800	Enhancers	Ovary	ovary
47	chr1:57036800-57039000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:57036800-57039200	Enhancers	Brain Anterior Caudate	brain
49	chr1:57036800-57039600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:57036800-57041600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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