Variant report

Variant	rs2660303
Chromosome Location	chr1:98513144-98513145
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:98512607-98517309	SK-N-SH	brain:	n/a	chr1:98516804-98516823
2	MXI1	chr1:98508914-98517058	SK-N-SH	brain:	n/a	n/a
3	REST	chr1:98512461-98515881	H1-neurons	neurons:	n/a	chr1:98514403-98514411 chr1:98513943-98513957

Variant related genes	Relation type
MIR137HG	TF binding region

Extended variants
information (count: 127 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10747489	0.85[JPT][hapmap]
rs10747491	1.00[JPT][hapmap]
rs10747492	1.00[JPT][hapmap]
rs10747495	0.80[ASN][1000 genomes]
rs10747496	0.80[ASN][1000 genomes]
rs10783082	0.80[ASN][1000 genomes]
rs10875112	1.00[JPT][hapmap]
rs10875113	1.00[JPT][hapmap]
rs10875118	1.00[JPT][hapmap]
rs10875125	0.80[ASN][1000 genomes]
rs11165920	1.00[JPT][hapmap]
rs11165921	1.00[JPT][hapmap]
rs1198571	0.80[ASN][1000 genomes]
rs1198572	0.80[ASN][1000 genomes]
rs1198573	0.80[ASN][1000 genomes]
rs1198574	0.80[ASN][1000 genomes]
rs1198591	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1198592	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1198593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1198594	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12062845	1.00[JPT][hapmap]
rs12067700	1.00[JPT][hapmap]
rs12077442	1.00[JPT][hapmap]
rs12406713	1.00[JPT][hapmap]
rs1628294	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1702293	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1702294	0.80[ASN][1000 genomes]
rs17379561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1782810	0.80[ASN][1000 genomes]
rs1782811	0.80[ASN][1000 genomes]
rs1782813	0.80[ASN][1000 genomes]
rs1782815	0.80[ASN][1000 genomes]
rs1801265	1.00[JPT][hapmap]
rs1892549	0.80[ASN][1000 genomes]
rs1892550	0.80[ASN][1000 genomes]
rs1892551	0.80[ASN][1000 genomes]
rs1892552	0.80[ASN][1000 genomes]
rs1938558	0.80[ASN][1000 genomes]
rs1938559	0.80[ASN][1000 genomes]
rs1938560	0.80[ASN][1000 genomes]
rs1938561	0.80[ASN][1000 genomes]
rs1938562	0.80[ASN][1000 genomes]
rs1938564	0.80[ASN][1000 genomes]
rs1938565	0.80[ASN][1000 genomes]
rs1938567	0.80[ASN][1000 genomes]
rs1938568	0.80[ASN][1000 genomes]
rs1938569	0.80[ASN][1000 genomes]
rs1938571	0.80[ASN][1000 genomes]
rs2022865	0.80[ASN][1000 genomes]
rs2154402	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2154403	0.80[ASN][1000 genomes]
rs2391873	0.80[ASN][1000 genomes]
rs2391902	0.80[ASN][1000 genomes]
rs2391903	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2391904	0.80[ASN][1000 genomes]
rs2660304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2802530	0.82[EUR][1000 genomes]
rs2802531	0.82[EUR][1000 genomes]
rs2802532	0.82[EUR][1000 genomes]
rs2893376	0.80[ASN][1000 genomes]
rs4245673	0.80[ASN][1000 genomes]
rs4246515	1.00[JPT][hapmap]
rs4292998	0.80[ASN][1000 genomes]
rs4372296	1.00[JPT][hapmap]
rs4379706	1.00[JPT][hapmap]
rs4394693	1.00[JPT][hapmap]
rs4394694	1.00[JPT][hapmap]
rs4411173	0.80[ASN][1000 genomes]
rs4421623	0.82[JPT][hapmap]
rs4423049	1.00[JPT][hapmap]
rs4456128	1.00[JPT][hapmap]
rs4477335	0.80[ASN][1000 genomes]
rs4480407	0.80[ASN][1000 genomes]
rs4506495	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4523551	1.00[JPT][hapmap]
rs4523552	0.85[JPT][hapmap]
rs4573558	0.80[ASN][1000 genomes]
rs4584446	0.80[ASN][1000 genomes]
rs4598523	1.00[JPT][hapmap]
rs4634961	0.80[ASN][1000 genomes]
rs4950117	0.80[ASN][1000 genomes]
rs4950118	0.80[ASN][1000 genomes]
rs4950119	0.80[ASN][1000 genomes]
rs4950120	0.80[ASN][1000 genomes]
rs4970722	1.00[JPT][hapmap]
rs5005705	0.80[ASN][1000 genomes]
rs61785888	0.80[ASN][1000 genomes]
rs61786696	0.86[EUR][1000 genomes]
rs61786697	0.86[EUR][1000 genomes]
rs6604093	1.00[JPT][hapmap]
rs6677116	1.00[JPT][hapmap]
rs6692580	1.00[JPT][hapmap]
rs6703588	1.00[JPT][hapmap]
rs7418577	1.00[JPT][hapmap]
rs7524038	1.00[JPT][hapmap]
rs9324380	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9324381	0.80[ASN][1000 genomes]
rs9324382	0.80[ASN][1000 genomes]
rs9324383	0.80[ASN][1000 genomes]
rs9324384	0.80[ASN][1000 genomes]
rs9324385	0.80[ASN][1000 genomes]
rs9324386	0.80[ASN][1000 genomes]
rs9324387	0.80[ASN][1000 genomes]
rs9324388	0.80[ASN][1000 genomes]
rs9324389	0.80[ASN][1000 genomes]
rs9440288	0.80[ASN][1000 genomes]
rs9440293	0.80[ASN][1000 genomes]
rs9440393	0.80[ASN][1000 genomes]
rs9658841	0.80[ASN][1000 genomes]
rs9659624	0.80[ASN][1000 genomes]
rs9661157	0.80[ASN][1000 genomes]
rs9661794	1.00[JPT][hapmap]
rs9662719	1.00[JPT][hapmap]
rs9662870	1.00[JPT][hapmap]
rs9724773	0.80[ASN][1000 genomes]
rs9725319	0.80[ASN][1000 genomes]
rs9727548	1.00[JPT][hapmap]
rs9727941	0.80[ASN][1000 genomes]
rs9727976	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1009621	chr1:98435638-98599284	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv871230	chr1:98436232-98564736	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
6	nsv470729	chr1:98461443-98564736	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv546874	chr1:98461443-98564736	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
8	nsv830736	chr1:98488491-98663726	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:98509600-98514600	Active TSS	Brain Angular Gyrus	brain
2	chr1:98512000-98514400	Weak transcription	Right Atrium	heart
3	chr1:98512200-98513800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:98512200-98513800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
5	chr1:98512200-98514000	Weak transcription	NH-A	brain
6	chr1:98512200-98514200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:98512200-98514200	Weak transcription	HSMMtube	muscle
8	chr1:98512200-98515000	Bivalent/Poised TSS	Fetal Brain Female	brain
9	chr1:98512200-98515200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr1:98512400-98513400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:98512400-98513600	Weak transcription	NHLF	lung
12	chr1:98512400-98513800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:98512400-98513800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:98512400-98513800	Weak transcription	HSMM	muscle
15	chr1:98512400-98514000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:98512400-98514000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:98512400-98514000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:98512400-98514000	Weak transcription	HMEC	breast
19	chr1:98512400-98514000	Weak transcription	HUVEC	blood vessel
20	chr1:98512400-98514000	Weak transcription	Osteobl	bone
21	chr1:98512400-98514400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:98512400-98514800	Active TSS	Brain Anterior Caudate	brain
23	chr1:98512600-98513600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:98512600-98514000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:98512600-98514000	Weak transcription	NHDF-Ad	bronchial
26	chr1:98512600-98514600	Active TSS	Fetal Brain Male	brain
27	chr1:98513000-98513200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
28	chr1:98513000-98514000	Weak transcription	A549	lung
29	chr1:98513000-98515400	Bivalent/Poised TSS	Fetal Intestine Large	intestine

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