Variant report

Variant	rs10005989
Chromosome Location	chr4:56405206-56405207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:56399354..56402784-chr4:56403627..56405786,3	K562	blood:
2	chr4:56403772..56408020-chr4:56410640..56413640,7	MCF-7	breast:
3	chr4:56400733..56405885-chr4:56406271..56410110,5	K562	blood:

Variant related genes	Relation type
ENSG00000134852	Chromatin interaction
ENSG00000272969	Chromatin interaction
ENSG00000223305	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10002541	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10009593	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016506	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026692	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10034433	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1011095	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs10462035	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133376	0.91[CEU][hapmap]
rs11133379	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133382	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11133383	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133394	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11133399	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11726609	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733864	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735267	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11931061	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11939815	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947476	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11947623	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12646078	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12647034	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13102385	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13121235	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13128582	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13138697	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13152650	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522106	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522107	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522108	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522110	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1522111	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17085889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873092	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1965467	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1980273	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2130036	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2140077	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2177127	1.00[CEU][hapmap]
rs2177129	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412646	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412647	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412663	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28445925	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28448438	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28463765	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28469692	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28514423	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28525309	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28572116	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28582059	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28670674	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28673496	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28713343	0.81[EUR][1000 genomes]
rs28790098	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899037	0.87[CEU][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs35767091	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3736544	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736545	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805147	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805152	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3805154	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817444	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828481	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4371676	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4580704	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473005	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs480479	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes]
rs4864998	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865008	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4865010	1.00[CEU][hapmap]
rs4865018	0.88[CEU][hapmap]
rs501679	0.91[CEU][hapmap]
rs564762	0.80[EUR][1000 genomes]
rs576779	0.86[AMR][1000 genomes]
rs59804446	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60797008	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60992571	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62303714	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62309727	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554280	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6554286	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554292	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6810948	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811520	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6812042	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815516	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817267	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6817663	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6819660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824057	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824955	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6825994	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6829182	0.95[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6832769	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6834676	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837710	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839788	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846427	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6850524	0.81[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6851838	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6853192	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726967	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7660054	1.00[CEU][hapmap]
rs7660808	0.81[EUR][1000 genomes]
rs7667849	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668147	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7670225	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673908	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677526	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7684810	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs819271	0.91[CEU][hapmap]
rs9312662	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9684708	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9993675	0.91[CEU][hapmap]
rs9997288	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9998038	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9998146	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56361600-56411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:56391600-56405600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:56391600-56405600	Weak transcription	Osteobl	bone
4	chr4:56391600-56405800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:56391600-56408800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:56391600-56409400	Weak transcription	NHDF-Ad	bronchial
7	chr4:56391800-56409400	Weak transcription	HMEC	breast
8	chr4:56391800-56409400	Weak transcription	NHEK	skin
9	chr4:56391800-56409600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:56393200-56408000	Weak transcription	K562	blood
11	chr4:56396200-56406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:56396800-56411600	Weak transcription	Psoas Muscle	Psoas
13	chr4:56399600-56411600	Weak transcription	Left Ventricle	heart
14	chr4:56399800-56411000	Weak transcription	Brain Substantia Nigra	brain
15	chr4:56400000-56410200	Weak transcription	Fetal Intestine Small	intestine
16	chr4:56400800-56406800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:56400800-56409600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:56401000-56409400	Weak transcription	HSMM	muscle
19	chr4:56401000-56409600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:56401000-56411400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:56401200-56410000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:56401200-56411800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:56401600-56410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:56402400-56409400	Weak transcription	Fetal Heart	heart
25	chr4:56402800-56409600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:56402800-56410600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:56402800-56411600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr4:56403000-56406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:56403000-56411400	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:56403200-56406800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:56403400-56405600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr4:56403400-56405800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:56403600-56408000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:56403800-56405800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr4:56403800-56406200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:56403800-56410400	Weak transcription	Fetal Stomach	stomach
37	chr4:56403800-56411800	Weak transcription	Lung	lung
38	chr4:56404000-56405600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr4:56404000-56405800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr4:56404000-56406200	Enhancers	Dnd41	blood
41	chr4:56404200-56405600	Enhancers	Primary T cells from cord blood	blood
42	chr4:56404200-56405600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr4:56404200-56405600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr4:56404200-56409400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:56404400-56405800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr4:56404600-56406800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr4:56404600-56410200	Weak transcription	Fetal Lung	lung
48	chr4:56405000-56405600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:56405000-56405600	Enhancers	Fetal Thymus	thymus
50	chr4:56405000-56405600	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links