Variant report

Variant	rs41266056
Chromosome Location	chr1:174671151-174671152
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs55833532	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55896504	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55926112	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56391203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58401153	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60449770	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6658058	1.00[ASN][1000 genomes]
rs6691555	1.00[ASN][1000 genomes]
rs6691857	1.00[ASN][1000 genomes]
rs74126812	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126813	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126815	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126817	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126818	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126819	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126820	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126822	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126823	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126824	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126826	1.00[AMR][1000 genomes]
rs74126827	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126828	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74126832	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126833	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126834	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126837	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126839	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126841	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126844	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126845	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543595	1.00[ASN][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	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41266056	RC3H1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174607600-174677800	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174646800-174677600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:174646800-174680400	Weak transcription	Ovary	ovary
4	chr1:174651800-174673000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:174651800-174677400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:174652400-174677400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:174652400-174678800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:174660600-174677600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:174662000-174673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:174665800-174677400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:174665800-174680000	Weak transcription	Fetal Intestine Large	intestine
12	chr1:174665800-174682600	Weak transcription	Left Ventricle	heart
13	chr1:174666000-174677800	Weak transcription	Primary T cells from cord blood	blood
14	chr1:174668400-174682600	Weak transcription	Gastric	stomach
15	chr1:174669400-174671200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:174669400-174671400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:174669600-174684000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:174669800-174672400	Weak transcription	K562	blood
19	chr1:174669800-174676000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:174670000-174676000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:174670200-174673800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:174670200-174675800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:174670400-174671200	Weak transcription	NHDF-Ad	bronchial
24	chr1:174670800-174671200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:174670800-174671200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:174670800-174671400	Genic enhancers	GM12878-XiMat	blood
27	chr1:174670800-174676000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:174671000-174671400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:174671000-174671400	Enhancers	Cortex derived primary cultured neurospheres	brain

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