Variant report

Variant	rs1889229
Chromosome Location	chr1:98262653-98262654
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX7-2	chr1:98262477-98262851	ENSG00000235777.1

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10157611	0.93[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1023245	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034215	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034216	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1034217	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493894	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493895	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493896	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747485	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747486	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747487	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783076	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875105	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875106	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875108	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875109	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165908	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs11165913	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059052	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406000	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12406752	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565244	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739159	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333717	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17378671	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17379095	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931063	0.82[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931064	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931066	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963206	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974203	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974204	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984091	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34486749	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329543	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537601	0.87[CEU][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61786604	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61786605	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675325	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676451	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685266	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703307	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527085	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538995	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv871740	chr1:98165091-98322379	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv546869	chr1:98253405-98328093	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98183600-98279600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:98240400-98309800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:98242200-98291600	Weak transcription	Dnd41	blood
4	chr1:98243400-98272600	Weak transcription	Liver	Liver
5	chr1:98248600-98310600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:98250800-98264000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:98255800-98310800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:98256400-98264000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:98257200-98315200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:98257400-98262800	Weak transcription	HSMM	muscle
11	chr1:98257400-98263000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:98257400-98267600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:98257600-98310200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:98258000-98267800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:98258000-98291400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:98258200-98293600	Weak transcription	Primary T cells from cord blood	blood
17	chr1:98258400-98285600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:98258600-98267000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:98261400-98264200	Enhancers	HUVEC	blood vessel
20	chr1:98261600-98264000	Enhancers	Rectal Smooth Muscle	rectum
21	chr1:98262000-98263400	Enhancers	Fetal Heart	heart
22	chr1:98262200-98262800	Enhancers	Brain Substantia Nigra	brain
23	chr1:98262200-98263000	Enhancers	Stomach Smooth Muscle	stomach
24	chr1:98262200-98263200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr1:98262200-98263200	Enhancers	Colon Smooth Muscle	Colon
26	chr1:98262200-98263200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr1:98262200-98263400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:98262200-98263400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:98262200-98263400	Enhancers	Fetal Brain Female	brain
30	chr1:98262200-98263600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:98262400-98262800	Enhancers	Brain Hippocampus Middle	brain
32	chr1:98262400-98263000	Enhancers	Stomach Mucosa	stomach
33	chr1:98262400-98263200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:98262400-98263200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:98262400-98263200	Enhancers	Fetal Intestine Large	intestine
36	chr1:98262400-98263200	Enhancers	Fetal Lung	lung
37	chr1:98262400-98263600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:98262400-98263600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:98262400-98264000	Enhancers	Osteobl	bone
40	chr1:98262600-98263200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr1:98262600-98263800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:98262600-98264000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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