Variant report

Variant	rs56943475
Chromosome Location	chr1:176122850-176122851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10494499	1.00[ASN][1000 genomes]
rs11579181	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579291	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11583071	0.93[AMR][1000 genomes]
rs11583207	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11583991	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11586568	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11587051	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11587254	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587785	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588361	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11588480	0.94[EUR][1000 genomes]
rs11590045	0.87[AMR][1000 genomes]
rs12403794	1.00[ASN][1000 genomes]
rs17351933	1.00[ASN][1000 genomes]
rs17352072	0.86[ASN][1000 genomes]
rs17354252	1.00[ASN][1000 genomes]
rs56125427	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56192244	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56949697	0.87[AMR][1000 genomes]
rs61821028	1.00[ASN][1000 genomes]
rs61822662	0.86[ASN][1000 genomes]
rs74127185	1.00[ASN][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	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
3	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
4	nsv548246	chr1:176043797-176136273	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176054400-176131600	Weak transcription	NH-A	brain
2	chr1:176055000-176141600	Weak transcription	Hela-S3	cervix
3	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
4	chr1:176069000-176139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:176069200-176123200	Weak transcription	Osteobl	bone
6	chr1:176069200-176126600	Weak transcription	HMEC	breast
7	chr1:176069200-176138800	Weak transcription	HUVEC	blood vessel
8	chr1:176070400-176126400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
10	chr1:176072000-176140600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:176072800-176126600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:176076200-176126000	Weak transcription	Ovary	ovary
13	chr1:176076200-176127800	Weak transcription	Esophagus	oesophagus
14	chr1:176083000-176126000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:176085400-176142400	Weak transcription	Lung	lung
16	chr1:176085600-176126000	Weak transcription	Fetal Stomach	stomach
17	chr1:176085600-176128600	Weak transcription	Placenta	Placenta
18	chr1:176090800-176126600	Weak transcription	Fetal Brain Male	brain
19	chr1:176094800-176126200	Weak transcription	Fetal Brain Female	brain
20	chr1:176094800-176126400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:176095600-176130200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:176096000-176138800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:176100400-176126400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
25	chr1:176101400-176126600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:176102800-176126400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:176102800-176130000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:176102800-176130600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:176103000-176125800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:176103200-176126600	Weak transcription	HSMMtube	muscle
31	chr1:176103400-176123400	Weak transcription	K562	blood
32	chr1:176103400-176126200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:176103400-176127400	Weak transcription	Fetal Heart	heart
34	chr1:176106000-176126400	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:176107600-176126600	Weak transcription	Brain Hippocampus Middle	brain
36	chr1:176108000-176123200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:176108000-176124600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:176108000-176126600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:176108600-176129800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:176109800-176123400	Weak transcription	Brain Germinal Matrix	brain
41	chr1:176110600-176123800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:176110600-176164000	Weak transcription	NHLF	lung
43	chr1:176111200-176126000	Weak transcription	Small Intestine	intestine
44	chr1:176111800-176126600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:176111800-176127400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:176111800-176139400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:176113000-176126400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:176114800-176123800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:176115200-176125600	Weak transcription	Fetal Lung	lung
50	chr1:176115200-176127200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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