Variant report

Variant	rs4601543
Chromosome Location	chr1:176030351-176030352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10494499	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10798427	0.84[EUR][1000 genomes]
rs10798428	0.84[EUR][1000 genomes]
rs11576862	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580753	1.00[ASN][1000 genomes]
rs11583071	1.00[ASN][1000 genomes]
rs11584481	1.00[ASN][1000 genomes]
rs11588480	1.00[ASN][1000 genomes]
rs11590045	1.00[ASN][1000 genomes]
rs12038027	0.82[EUR][1000 genomes]
rs12403794	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12404181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357337	0.82[EUR][1000 genomes]
rs17351808	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17351933	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17352072	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17354252	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2481635	0.83[EUR][1000 genomes]
rs2481647	0.89[EUR][1000 genomes]
rs2481651	0.91[EUR][1000 genomes]
rs2481657	0.91[EUR][1000 genomes]
rs2502822	0.91[EUR][1000 genomes]
rs2502826	0.91[EUR][1000 genomes]
rs2861630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129061	0.91[EUR][1000 genomes]
rs4307526	0.86[EUR][1000 genomes]
rs4314844	0.86[EUR][1000 genomes]
rs4460596	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4650934	0.82[EUR][1000 genomes]
rs56051510	1.00[ASN][1000 genomes]
rs56198111	1.00[ASN][1000 genomes]
rs56949697	1.00[ASN][1000 genomes]
rs60719126	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60964243	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61186664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820953	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820960	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820965	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820968	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61820999	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61821007	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821009	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821028	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61822662	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61822767	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425368	0.84[EUR][1000 genomes]
rs6680309	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693947	0.83[AMR][1000 genomes]
rs6704509	0.86[EUR][1000 genomes]
rs74127150	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74127154	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74127185	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7524972	0.82[EUR][1000 genomes]
rs7545043	0.83[EUR][1000 genomes]
rs7545639	0.86[EUR][1000 genomes]
rs7554913	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9783047	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv872564	chr1:176027978-176102808	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
3	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:175989800-176036400	Weak transcription	Pancreas	Pancrea
6	chr1:175994200-176065200	Weak transcription	Psoas Muscle	Psoas
7	chr1:176004000-176036400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:176004200-176039800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:176006000-176045200	Weak transcription	GM12878-XiMat	blood
10	chr1:176006200-176049000	Weak transcription	HSMM	muscle
11	chr1:176007800-176066400	Weak transcription	Fetal Brain Male	brain
12	chr1:176010200-176048000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:176010400-176066000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:176012200-176044800	Weak transcription	Fetal Stomach	stomach
15	chr1:176012200-176045200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:176012200-176045200	Weak transcription	Esophagus	oesophagus
17	chr1:176012200-176045200	Weak transcription	Fetal Lung	lung
18	chr1:176012400-176036400	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:176012400-176036400	Weak transcription	Gastric	stomach
20	chr1:176012400-176036400	Weak transcription	Left Ventricle	heart
21	chr1:176012400-176036400	Weak transcription	Spleen	Spleen
22	chr1:176012400-176045400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:176012400-176045800	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:176012400-176048200	Weak transcription	Ovary	ovary
25	chr1:176012400-176048200	Weak transcription	Thymus	Thymus
26	chr1:176012400-176062800	Weak transcription	Lung	lung
27	chr1:176012400-176065800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:176012800-176030400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:176012800-176036800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:176012800-176038000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:176012800-176040000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:176012800-176042600	Weak transcription	Liver	Liver
33	chr1:176012800-176047000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:176013000-176040000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:176013000-176045000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:176013400-176040000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:176013600-176037600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:176013600-176040000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:176014400-176039800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:176014400-176045200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr1:176015400-176038000	Weak transcription	Dnd41	blood
42	chr1:176015400-176039000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:176015400-176040200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:176015600-176040000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:176017000-176036400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:176017200-176036400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:176017600-176030400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:176020800-176033400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:176020800-176037600	Weak transcription	Adipose Nuclei	Adipose
50	chr1:176021600-176045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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