Variant report

Variant	rs6664740
Chromosome Location	chr1:226083197-226083198
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226076187..226078341-chr1:226083118..226085754,2	K562	blood:
2	chr1:226061743..226065093-chr1:226081244..226084907,3	MCF-7	breast:
3	chr1:226080997..226083226-chr1:226084406..226086533,2	K562	blood:
4	chr1:225968570..225970564-chr1:226082071..226083838,2	K562	blood:
5	chr1:226073077..226074812-chr1:226081952..226084486,2	K562	blood:
6	chr1:226067224..226072522-chr1:226081850..226086228,5	K562	blood:
7	chr1:226073359..226078692-chr1:226082383..226086507,6	MCF-7	breast:
8	chr1:226082392..226086570-chr1:226107502..226111171,5	MCF-7	breast:
9	chr1:226068047..226071599-chr1:226082710..226085024,3	K562	blood:
10	chr1:226075279..226077934-chr1:226082021..226084716,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000243709	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10047091	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10158952	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12061043	1.00[EUR][1000 genomes]
rs12071072	1.00[EUR][1000 genomes]
rs12071104	1.00[EUR][1000 genomes]
rs12074209	1.00[EUR][1000 genomes]
rs12074247	1.00[EUR][1000 genomes]
rs12075664	0.90[EUR][1000 genomes]
rs2236143	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271544	0.95[EUR][1000 genomes]
rs2292556	0.90[EUR][1000 genomes]
rs2292559	0.90[EUR][1000 genomes]
rs2292561	0.90[EUR][1000 genomes]
rs2292568	0.87[EUR][1000 genomes]
rs28384446	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28384447	0.86[EUR][1000 genomes]
rs28384448	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28384449	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3738050	0.90[EUR][1000 genomes]
rs3738051	0.90[EUR][1000 genomes]
rs3753663	0.90[EUR][1000 genomes]
rs3753666	0.92[EUR][1000 genomes]
rs3753668	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753670	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766935	0.90[EUR][1000 genomes]
rs3766936	0.90[EUR][1000 genomes]
rs3766937	0.90[EUR][1000 genomes]
rs3766940	0.95[EUR][1000 genomes]
rs3766941	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806257	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806258	1.00[EUR][1000 genomes]
rs41310561	1.00[EUR][1000 genomes]
rs4149227	0.87[EUR][1000 genomes]
rs4149228	0.90[EUR][1000 genomes]
rs4149230	0.90[EUR][1000 genomes]
rs45467394	0.84[EUR][1000 genomes]
rs56231004	1.00[EUR][1000 genomes]
rs56325807	0.90[EUR][1000 genomes]
rs57095220	0.90[EUR][1000 genomes]
rs57932384	0.90[EUR][1000 genomes]
rs59728172	0.90[EUR][1000 genomes]
rs60847271	0.95[EUR][1000 genomes]
rs60943392	0.90[EUR][1000 genomes]
rs61033712	0.90[EUR][1000 genomes]
rs61227102	0.90[EUR][1000 genomes]
rs61295362	0.90[EUR][1000 genomes]
rs74150536	0.90[EUR][1000 genomes]
rs7514448	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7516538	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
10	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:226076800-226084600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:226077000-226085200	Weak transcription	Spleen	Spleen
4	chr1:226077000-226099000	Weak transcription	Right Atrium	heart
5	chr1:226077400-226084600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:226078600-226084000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:226078800-226084200	Weak transcription	A549	lung
8	chr1:226078800-226084800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:226078800-226086800	Weak transcription	Fetal Stomach	stomach
10	chr1:226079000-226084400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:226079000-226084600	Weak transcription	Colonic Mucosa	Colon
12	chr1:226079000-226084800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:226079200-226083600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:226079200-226084400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:226079200-226084600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:226079200-226085000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:226079200-226085800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:226079600-226084200	Weak transcription	K562	blood
19	chr1:226079600-226084400	Weak transcription	NHEK	skin
20	chr1:226079600-226084600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:226079600-226084600	Weak transcription	Fetal Intestine Large	intestine
22	chr1:226079800-226083600	Weak transcription	Gastric	stomach
23	chr1:226079800-226083800	Weak transcription	Liver	Liver
24	chr1:226079800-226083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:226079800-226084200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:226079800-226084200	Weak transcription	HepG2	liver
27	chr1:226079800-226084400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:226079800-226084400	Weak transcription	HMEC	breast
29	chr1:226079800-226084600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:226079800-226084600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:226079800-226084600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:226079800-226084600	Weak transcription	Hela-S3	cervix
33	chr1:226079800-226084800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:226079800-226085000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:226080400-226083600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:226080400-226083600	Weak transcription	Pancreas	Pancrea
37	chr1:226080400-226083600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:226080400-226083600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:226080400-226084200	Weak transcription	Stomach Mucosa	stomach
40	chr1:226081200-226084200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:226081400-226084600	Enhancers	Primary T cells fromperipheralblood	blood
42	chr1:226081600-226084200	Enhancers	Primary T cells from cord blood	blood
43	chr1:226081600-226084600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:226082000-226084200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:226082000-226085600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:226082400-226083600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:226082400-226083600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:226082400-226083600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:226082400-226084600	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links