Variant report

Variant	rs4653515
Chromosome Location	chr1:227760506-227760507
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227758119..227760802-chr16:33923322..33925835,2	MCF-7	breast:
2	chr1:227747468..227754046-chr1:227756230..227762193,11	K562	blood:
3	chr1:227751815..227753395-chr1:227758245..227760827,2	K562	blood:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction
ENSG00000202264	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1021553	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1021554	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10495276	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799423	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10799431	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799432	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10799433	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799434	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799435	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916158	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10916159	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10916165	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916175	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916176	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916179	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916182	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916183	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916184	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916185	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916187	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11484723	0.90[EUR][1000 genomes]
rs11580570	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12023298	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12025815	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040302	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12070002	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12070036	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12079123	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12080321	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12132444	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12740317	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407718	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1495842	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1495845	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1495847	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1845758	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2018401	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2088210	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088211	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088212	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088214	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2093609	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2093610	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2132367	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2201571	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2644140	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28407112	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2935145	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2935146	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2935147	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2935152	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2935155	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999741	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2999743	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999744	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999745	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2999746	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010183	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010186	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010190	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010191	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010192	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010193	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010194	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3010195	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3010196	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4359006	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653512	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653514	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653848	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653849	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4653850	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4653853	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6664682	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6671825	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697867	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7512348	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7523915	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7528094	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539914	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7542685	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7551459	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs903683	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903684	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs903690	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903697	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs951083	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs976959	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv947073	chr1:227755113-227760558	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv945340	chr1:227758923-227760558	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227752000-227766800	Weak transcription	Ovary	ovary
2	chr1:227752200-227763200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:227752200-227774400	Weak transcription	Aorta	Aorta
4	chr1:227752400-227763000	Weak transcription	Stomach Mucosa	stomach
5	chr1:227752400-227763800	Weak transcription	HSMMtube	muscle
6	chr1:227752400-227766800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:227752400-227780600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:227753600-227763000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:227754400-227783600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:227756800-227762400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:227758400-227761400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:227759400-227761000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr1:227759800-227760600	ZNF genes & repeats	Fetal Lung	lung
14	chr1:227759800-227760600	Genic enhancers	Left Ventricle	heart
15	chr1:227759800-227760800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:227759800-227760800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:227759800-227760800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr1:227759800-227760800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:227759800-227760800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:227759800-227760800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr1:227759800-227760800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
22	chr1:227759800-227760800	Genic enhancers	K562	blood
23	chr1:227759800-227761000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:227759800-227761000	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr1:227759800-227761800	ZNF genes & repeats	Primary B cells from cord blood	blood
26	chr1:227760000-227760600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:227760000-227760600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:227760000-227760600	Strong transcription	Fetal Intestine Large	intestine
29	chr1:227760000-227760600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr1:227760000-227760600	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr1:227760000-227760600	Genic enhancers	Pancreas	Pancrea
32	chr1:227760000-227760600	ZNF genes & repeats	Thymus	Thymus
33	chr1:227760000-227760800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
34	chr1:227760000-227760800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:227760000-227760800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:227760000-227760800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
37	chr1:227760000-227760800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:227760000-227760800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:227760000-227760800	ZNF genes & repeats	Esophagus	oesophagus
40	chr1:227760000-227760800	ZNF genes & repeats	Fetal Intestine Small	intestine
41	chr1:227760000-227760800	ZNF genes & repeats	Fetal Stomach	stomach
42	chr1:227760000-227760800	ZNF genes & repeats	Gastric	stomach
43	chr1:227760000-227760800	Enhancers	Right Ventricle	heart
44	chr1:227760000-227760800	ZNF genes & repeats	Spleen	Spleen
45	chr1:227760000-227760800	ZNF genes & repeats	NHEK	skin
46	chr1:227760000-227761000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
47	chr1:227760200-227760600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
48	chr1:227760200-227760800	ZNF genes & repeats	Lung	lung
49	chr1:227760200-227760800	Enhancers	Psoas Muscle	Psoas
50	chr1:227760200-227761000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links