Variant report

Variant	rs10888975
Chromosome Location	chr1:56956236-56956237
allele	A/G
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]
rs10789023	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10789024	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888976	0.85[CHD][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.89[YRI][hapmap]
rs11206810	0.82[EUR][1000 genomes]
rs11206814	0.84[EUR][1000 genomes]
rs11206816	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11206817	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11206818	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11206823	0.86[ASN][1000 genomes]
rs11206825	0.90[ASN][1000 genomes]
rs11206830	0.85[CHD][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11206831	0.83[EUR][1000 genomes]
rs11206832	0.83[EUR][1000 genomes]
rs11589246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1930761	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4628	0.82[JPT][hapmap]
rs4912291	0.87[ASN][1000 genomes]
rs61772590	0.83[EUR][1000 genomes]
rs7525717	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7528118	0.82[TSI][hapmap]
rs8016	0.97[TSI][hapmap];0.84[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:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56943800-56957000	Weak transcription	HSMM	muscle
2	chr1:56943800-56957200	Weak transcription	Psoas Muscle	Psoas
3	chr1:56943800-56957400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:56943800-56957600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:56943800-56959400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:56944000-56957400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:56944400-56957200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:56944400-56957200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:56944400-56959600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:56944600-56956400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:56944600-56957400	Weak transcription	Lung	lung
12	chr1:56944600-56957800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:56944800-56957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:56944800-56957200	Weak transcription	Fetal Stomach	stomach
15	chr1:56944800-56957200	Weak transcription	Right Ventricle	heart
16	chr1:56944800-56957400	Weak transcription	Left Ventricle	heart
17	chr1:56944800-56960800	Weak transcription	Fetal Kidney	kidney
18	chr1:56945200-56957200	Weak transcription	Placenta	Placenta
19	chr1:56945800-56957200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:56948800-56965200	Weak transcription	Brain Angular Gyrus	brain
21	chr1:56950400-56959400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:56951000-56959000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:56951200-56957400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:56953600-56959400	Weak transcription	Aorta	Aorta
25	chr1:56954400-56957400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:56954600-56957000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:56955000-56957400	Weak transcription	Thymus	Thymus
28	chr1:56955200-56961000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:56955400-56960000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:56955600-56957800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:56955800-56956400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:56956000-56958400	Enhancers	HUVEC	blood vessel
33	chr1:56956000-56960800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:56956200-56956400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:56956200-56956400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:56956200-56956400	Enhancers	Brain Substantia Nigra	brain
37	chr1:56956200-56956400	Enhancers	Gastric	stomach
38	chr1:56956200-56956400	Enhancers	Ovary	ovary
39	chr1:56956200-56956400	Enhancers	Pancreas	Pancrea
40	chr1:56956200-56956400	Enhancers	Right Atrium	heart
41	chr1:56956200-56956600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:56956200-56956600	Enhancers	HepG2	liver
43	chr1:56956200-56957200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:56956200-56957400	Enhancers	Hela-S3	cervix
45	chr1:56956200-56957800	Enhancers	Small Intestine	intestine
46	chr1:56956200-56958200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:56956200-56958200	Enhancers	Brain Anterior Caudate	brain
48	chr1:56956200-56958800	Enhancers	Liver	Liver

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