Variant report

Variant	rs260087
Chromosome Location	chr15:99671760-99671761
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10902539	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12148328	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441651	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670216	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1670224	0.81[AMR][1000 genomes]
rs1670230	0.95[CEU][hapmap]
rs1670232	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1670233	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670234	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670244	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1670251	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1670253	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1670254	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1703762	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1703763	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1703766	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1703771	0.81[AMR][1000 genomes]
rs187755	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305445	0.86[CHD][hapmap]
rs260114	0.81[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2602016	0.95[CEU][hapmap];0.87[GIH][hapmap]
rs2602018	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs2602020	0.81[AMR][1000 genomes]
rs2602021	0.81[ASW][hapmap]
rs2602022	0.90[EUR][1000 genomes]
rs2602026	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.81[AMR][1000 genomes]
rs2602038	1.00[CEU][hapmap]
rs2623188	0.81[AMR][1000 genomes]
rs2623189	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2623190	0.81[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.81[AMR][1000 genomes]
rs2623191	0.81[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs2654967	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3210942	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3743248	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4573918	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4602019	0.81[CEU][hapmap]
rs4965217	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs55803543	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7163625	1.00[CEU][hapmap]
rs7183226	0.81[ASW][hapmap]
rs7183480	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs921578	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs260087	TTC23	cis	parietal	SCAN
rs260087	TTC23	cis	cerebellum	SCAN
rs260087	SYNM	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
2	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:99664200-99675800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:99664400-99678800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr15:99664400-99678800	Weak transcription	Brain Germinal Matrix	brain
6	chr15:99664600-99672600	Weak transcription	Small Intestine	intestine
7	chr15:99664600-99676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:99664600-99677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:99664600-99678800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:99664800-99672800	Weak transcription	Fetal Thymus	thymus
12	chr15:99664800-99682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:99665000-99676000	Genic enhancers	Colon Smooth Muscle	Colon
15	chr15:99665000-99676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:99665000-99676800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr15:99665000-99683800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr15:99665000-99714200	Weak transcription	NHEK	skin
19	chr15:99665200-99676000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:99665200-99677400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:99665200-99677400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:99665200-99677600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:99665200-99679400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:99665800-99671800	Strong transcription	Fetal Stomach	stomach
26	chr15:99665800-99676600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:99665800-99676800	Weak transcription	Ovary	ovary
28	chr15:99665800-99676800	Weak transcription	Spleen	Spleen
29	chr15:99665800-99677200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:99666000-99675200	Weak transcription	HSMM	muscle
31	chr15:99666000-99675400	Weak transcription	Osteobl	bone
32	chr15:99666000-99683000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:99666200-99675400	Weak transcription	NHDF-Ad	bronchial
34	chr15:99666200-99680400	Weak transcription	Fetal Brain Female	brain
35	chr15:99666200-99684200	Weak transcription	HSMMtube	muscle
36	chr15:99666400-99679800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:99666800-99673200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:99666800-99677200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:99666800-99677200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:99666800-99677400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:99667000-99673200	Strong transcription	Adipose Nuclei	Adipose
42	chr15:99667000-99673800	Weak transcription	Fetal Heart	heart
43	chr15:99667000-99676200	Genic enhancers	Rectal Smooth Muscle	rectum
44	chr15:99667200-99672800	Strong transcription	Placenta	Placenta
45	chr15:99667400-99673000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr15:99667400-99674000	Weak transcription	Psoas Muscle	Psoas
47	chr15:99667400-99674200	Weak transcription	Right Atrium	heart
48	chr15:99667400-99675000	Strong transcription	Hela-S3	cervix
49	chr15:99667600-99679200	Strong transcription	Fetal Muscle Leg	muscle
50	chr15:99668600-99672600	Strong transcription	Aorta	Aorta

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