Variant report

Variant	rs4497165
Chromosome Location	chr1:175962478-175962479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12402588	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12403164	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12407451	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12408191	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12408512	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409154	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12411139	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16849609	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17351760	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17351774	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17354043	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4265393	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4292913	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4498761	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55779970	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56346636	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57729493	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58539711	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59540069	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59801736	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60630667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820918	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61820933	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820935	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61820936	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61820954	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61820962	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61820963	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61820964	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820966	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820969	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61820971	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61820976	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61821000	0.88[EUR][1000 genomes]
rs61821005	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821006	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821032	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821033	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821035	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61821058	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61821059	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61822660	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61822661	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61822765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61822766	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61822768	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701833	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74127146	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74127162	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7553673	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175906400-175962600	Weak transcription	NH-A	brain
2	chr1:175946000-175996000	Weak transcription	HMEC	breast
3	chr1:175953800-175999600	Weak transcription	Colonic Mucosa	Colon
4	chr1:175954000-175963600	Weak transcription	Lung	lung
5	chr1:175954000-175977800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:175954000-175978000	Weak transcription	Left Ventricle	heart
7	chr1:175954000-175987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:175954600-175964600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:175954800-175963000	Weak transcription	Brain Anterior Caudate	brain
10	chr1:175954800-175968600	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:175955000-175963800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:175956000-175963000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:175956000-175963400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:175956200-175963600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:175957000-175981200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:175957400-175962800	Weak transcription	NHDF-Ad	bronchial
17	chr1:175957600-175977400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:175957600-175977400	Weak transcription	HSMM	muscle
19	chr1:175957800-175971200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:175958000-175962600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:175958000-175964000	Weak transcription	Primary T cells from cord blood	blood
23	chr1:175958000-175965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:175958000-175977200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:175958000-175977200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:175958000-175977400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:175958000-175987800	Weak transcription	Fetal Thymus	thymus
28	chr1:175958200-175978000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:175958400-175968200	Weak transcription	Fetal Lung	lung
30	chr1:175958600-175963000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:175958600-175964200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr1:175958600-175965200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:175958600-175977400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:175958600-175977400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:175958600-175977400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:175958600-175977400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:175958800-175965400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:175958800-175980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:175959000-175966200	Weak transcription	Liver	Liver
40	chr1:175959200-175977400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:175959400-175977400	Weak transcription	Dnd41	blood
42	chr1:175960000-175977400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:175960800-175963000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:175961000-175963400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:175961000-175971600	Weak transcription	Primary B cells from cord blood	blood
46	chr1:175961000-175977600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:175961200-175977600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:175961600-175962600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:175962000-175962600	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr1:175962400-175977800	Weak transcription	Primary hematopoietic stem cells	blood

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