Variant report

Variant	rs41310561
Chromosome Location	chr1:226076669-226076670
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226061864..226068048-chr1:226072871..226078674,7	MCF-7	breast:
2	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10047091	1.00[EUR][1000 genomes]
rs12061043	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12071072	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12071104	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12074209	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12074247	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12075664	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236143	0.97[EUR][1000 genomes]
rs2271544	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292556	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2292559	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292560	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2292561	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2292568	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28384446	0.92[EUR][1000 genomes]
rs28384447	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28384448	0.95[EUR][1000 genomes]
rs28384449	0.95[EUR][1000 genomes]
rs360084	0.91[ASN][1000 genomes]
rs360087	0.91[ASN][1000 genomes]
rs360089	0.91[ASN][1000 genomes]
rs3738050	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3738051	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753663	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753666	0.92[EUR][1000 genomes]
rs3753668	1.00[EUR][1000 genomes]
rs3753670	1.00[EUR][1000 genomes]
rs3766935	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766936	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766937	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766940	0.95[EUR][1000 genomes]
rs3766941	1.00[EUR][1000 genomes]
rs3806257	1.00[EUR][1000 genomes]
rs3806258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149227	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4149228	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4149230	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs45467394	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56231004	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56301120	0.90[ASN][1000 genomes]
rs56325807	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57095220	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57932384	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59728172	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60847271	0.95[EUR][1000 genomes]
rs60943392	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61033712	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61227102	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61295362	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6664740	1.00[EUR][1000 genomes]
rs74150536	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514448	1.00[EUR][1000 genomes]
rs7516538	1.00[EUR][1000 genomes]
rs805179	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226071000-226078600	Weak transcription	Lung	lung
2	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:226071200-226078200	Weak transcription	Gastric	stomach
4	chr1:226071200-226078200	Weak transcription	HMEC	breast
5	chr1:226071600-226076800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:226071800-226076800	Weak transcription	K562	blood
7	chr1:226071800-226078800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:226072000-226076800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:226072000-226081200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:226072000-226081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:226072000-226082000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:226073000-226077000	Strong transcription	Right Atrium	heart
13	chr1:226073200-226079800	Enhancers	Liver	Liver
14	chr1:226074200-226077000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr1:226074400-226076800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:226074400-226077200	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:226074800-226076800	Weak transcription	Fetal Intestine Large	intestine
18	chr1:226074800-226078800	Enhancers	Fetal Stomach	stomach
19	chr1:226075000-226076800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:226075200-226077200	Active TSS	Colonic Mucosa	Colon
21	chr1:226075400-226076800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:226075400-226079200	Enhancers	Ovary	ovary
23	chr1:226075600-226076800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:226075600-226076800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:226075800-226076800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr1:226075800-226077000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr1:226075800-226077600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr1:226075800-226079000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:226076000-226076800	Flanking Active TSS	Fetal Lung	lung
30	chr1:226076000-226076800	Enhancers	Right Ventricle	heart
31	chr1:226076000-226077000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:226076200-226076800	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr1:226076200-226078800	Enhancers	A549	lung
34	chr1:226076200-226079000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:226076400-226076800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:226076400-226076800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:226076400-226076800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:226076400-226077000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:226076400-226077000	Enhancers	Spleen	Spleen
40	chr1:226076400-226077200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:226076400-226077400	Flanking Bivalent TSS/Enh	HepG2	liver
42	chr1:226076400-226078000	Enhancers	Fetal Kidney	kidney
43	chr1:226076400-226079000	Enhancers	Placenta	Placenta
44	chr1:226076600-226076800	Active TSS	H9 Cell Line	embryonic stem cell
45	chr1:226076600-226076800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr1:226076600-226076800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
47	chr1:226076600-226077600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr1:226076600-226077800	Weak transcription	Small Intestine	intestine
49	chr1:226076600-226078600	Enhancers	Fetal Muscle Leg	muscle
50	chr1:226076600-226079000	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links