Variant report

Variant	rs7542598
Chromosome Location	chr1:62611149-62611150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10157504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805802	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123133	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677979	0.86[ASN][1000 genomes]
rs72677981	0.86[ASN][1000 genomes]
rs7513982	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514107	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546744	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012683	chr1:62587852-62643998	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
5	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:62566200-62614000	Weak transcription	Adipose Nuclei	Adipose
8	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
9	chr1:62580000-62611600	Weak transcription	Pancreas	Pancrea
10	chr1:62580200-62617200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:62588600-62622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:62593200-62621800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:62593400-62617600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
15	chr1:62594400-62614800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:62595000-62612600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:62595200-62614200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:62595200-62625200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:62595400-62614000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:62596000-62614000	Weak transcription	Left Ventricle	heart
21	chr1:62596000-62617800	Weak transcription	Aorta	Aorta
22	chr1:62596200-62614200	Weak transcription	Ovary	ovary
23	chr1:62598600-62614000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:62598800-62612600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:62599000-62616000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:62602800-62614000	Weak transcription	HMEC	breast
27	chr1:62603000-62614200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr1:62603800-62613800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:62603800-62617200	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:62603800-62617400	Weak transcription	Gastric	stomach
31	chr1:62603800-62617800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:62604000-62614000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:62604000-62614000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:62604600-62617800	Weak transcription	Esophagus	oesophagus
35	chr1:62605000-62631800	Weak transcription	Lung	lung
36	chr1:62605200-62614000	Weak transcription	Liver	Liver
37	chr1:62605200-62622400	Weak transcription	Fetal Brain Female	brain
38	chr1:62605200-62624400	Weak transcription	Right Atrium	heart
39	chr1:62605400-62613800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:62606000-62612600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:62606000-62617400	Weak transcription	A549	lung
42	chr1:62606400-62628600	Weak transcription	Stomach Mucosa	stomach
43	chr1:62606800-62614000	Weak transcription	Fetal Stomach	stomach
44	chr1:62607000-62612600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:62607000-62630000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:62608000-62618800	Weak transcription	Brain Germinal Matrix	brain
47	chr1:62608400-62613200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:62608400-62614000	Weak transcription	Right Ventricle	heart
49	chr1:62608400-62614000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:62608400-62617600	Weak transcription	Colon Smooth Muscle	Colon

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