Variant report

Variant	rs7553943
Chromosome Location	chr1:98330301-98330302
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10735795	0.89[ASW][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10747494	0.81[ASW][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10875119	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11165918	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11165926	0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1333721	0.91[YRI][hapmap]
rs1333722	1.00[EUR][1000 genomes]
rs17100628	0.81[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17117047	1.00[EUR][1000 genomes]
rs17117167	1.00[YRI][hapmap]
rs17117173	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17117175	1.00[YRI][hapmap]
rs17117176	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17117179	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17117181	0.81[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17117194	0.81[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17117198	1.00[YRI][hapmap]
rs17117203	1.00[YRI][hapmap]
rs17117207	0.91[YRI][hapmap]
rs17117211	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs17117214	0.90[YRI][hapmap]
rs17117218	0.91[YRI][hapmap]
rs17117228	0.91[YRI][hapmap]
rs17117234	0.91[YRI][hapmap]
rs17117236	0.83[AFR][1000 genomes]
rs17117251	0.81[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17117438	1.00[EUR][1000 genomes]
rs17117480	1.00[EUR][1000 genomes]
rs17117486	1.00[EUR][1000 genomes]
rs17117488	1.00[EUR][1000 genomes]
rs17117490	1.00[EUR][1000 genomes]
rs17117528	1.00[EUR][1000 genomes]
rs1855376	0.91[YRI][hapmap]
rs4269803	0.89[ASW][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4304628	0.89[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4348763	0.89[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4351683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4367807	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs4592283	1.00[EUR][1000 genomes]
rs4970718	0.90[AFR][1000 genomes]
rs55989986	1.00[EUR][1000 genomes]
rs56996093	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57429463	1.00[EUR][1000 genomes]
rs57957567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58211735	1.00[EUR][1000 genomes]
rs58260707	1.00[EUR][1000 genomes]
rs58615096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59161138	0.83[AFR][1000 genomes]
rs59429666	1.00[EUR][1000 genomes]
rs60366086	1.00[EUR][1000 genomes]
rs6604092	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6604119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74105297	1.00[EUR][1000 genomes]
rs74105460	1.00[EUR][1000 genomes]
rs74105461	0.83[AFR][1000 genomes]
rs74105462	0.83[AFR][1000 genomes]
rs74106015	1.00[EUR][1000 genomes]
rs74106140	1.00[EUR][1000 genomes]
rs74107712	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74107713	0.83[AFR][1000 genomes]
rs74108221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74108405	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74108407	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7511709	0.89[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7545029	0.89[ASW][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7546038	0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9324376	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9324377	1.00[EUR][1000 genomes]
rs9661407	1.00[ASW][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9727974	0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9729900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1012958	chr1:98081528-98864746	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv871472	chr1:98165091-98342417	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv870596	chr1:98165091-98365310	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv871625	chr1:98165091-98564736	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv871050	chr1:98187755-98365310	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1799805	chr1:98198206-98349028	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv871651	chr1:98200719-98365310	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv546870	chr1:98253405-98336823	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv546871	chr1:98253405-98337283	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv830725	chr1:98257894-98443497	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv934244	chr1:98260729-98415915	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv871376	chr1:98274132-98365310	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv871077	chr1:98274132-98541677	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
16	nsv462572	chr1:98283854-98347775	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv546872	chr1:98283854-98347775	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv546873	chr1:98283854-98348885	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv871224	chr1:98290577-98365310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv870944	chr1:98299475-98365310	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv2032	chr1:98319851-98369285	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv870727	chr1:98322379-98365310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98303200-98351000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:98309400-98367200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:98311600-98337800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:98311800-98350400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:98312200-98344400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:98315600-98337200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:98315800-98332200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:98316400-98346400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:98316400-98348000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:98316400-98349200	Weak transcription	NHDF-Ad	bronchial
11	chr1:98316600-98332200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:98319000-98330400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:98320800-98331800	Weak transcription	HSMM	muscle
14	chr1:98320800-98346400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr1:98320800-98351800	Weak transcription	Esophagus	oesophagus
16	chr1:98321000-98351800	Weak transcription	Left Ventricle	heart
17	chr1:98323400-98345800	Weak transcription	Liver	Liver
18	chr1:98323400-98351800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:98323600-98330400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:98323600-98331600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:98323600-98334600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:98329600-98330800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:98329800-98330400	Enhancers	Psoas Muscle	Psoas
24	chr1:98329800-98332200	Enhancers	Dnd41	blood
25	chr1:98330000-98330400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:98330000-98330600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:98330000-98330600	Flanking Active TSS	GM12878-XiMat	blood
28	chr1:98330000-98330800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:98330000-98330800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:98330000-98330800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:98330000-98330800	Enhancers	Thymus	Thymus
32	chr1:98330200-98330400	Enhancers	Brain Substantia Nigra	brain
33	chr1:98330200-98330600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:98330200-98330600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:98330200-98330800	Enhancers	Primary hematopoietic stem cells	blood
36	chr1:98330200-98330800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:98330200-98330800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:98330200-98330800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr1:98330200-98330800	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr1:98330200-98330800	Enhancers	Osteobl	bone
41	chr1:98330200-98331200	Enhancers	Primary T cells from cord blood	blood

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