Variant report

Variant	rs1530920
Chromosome Location	chr15:99710381-99710382
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12324187	0.81[CEU][hapmap]
rs12324825	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12591477	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12594336	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12595385	0.96[CEU][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12915572	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1377267	0.92[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.92[LWK][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1670237	0.81[MEX][hapmap]
rs1810091	0.81[CHD][hapmap];0.81[MEX][hapmap]
rs28517698	0.86[EUR][1000 genomes]
rs28612155	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28819101	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3803472	0.92[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4500700	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7170336	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174431	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs735823	0.83[GIH][hapmap]
rs8023421	0.81[CEU][hapmap]
rs8023490	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8026991	0.96[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029732	0.81[MEX][hapmap]
rs8031175	0.83[GIH][hapmap]
rs8032154	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8038002	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8038392	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8038732	0.81[AMR][1000 genomes]
rs9672800	0.92[CEU][hapmap]

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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1530920	TTC23	cis	multi-tissue	Pritchard
rs1530920	TTC23	cis	cerebellum	SCAN
rs1530920	SYNM	cis	cerebellum	SCAN
rs1530920	TTC23	cis	parietal	SCAN
rs1530920	SYNM	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99665000-99714200	Weak transcription	NHEK	skin
2	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
3	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:99692000-99717000	Weak transcription	HSMM	muscle
6	chr15:99694800-99711000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:99694800-99721200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:99694800-99732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:99694800-99732600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:99695200-99721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:99695200-99721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:99695200-99732400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:99696600-99710800	Weak transcription	HMEC	breast
14	chr15:99697000-99716800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
16	chr15:99697200-99712400	Weak transcription	Hela-S3	cervix
17	chr15:99699400-99731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:99700200-99710800	Weak transcription	Dnd41	blood
19	chr15:99700200-99731200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:99700400-99730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:99702200-99711000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:99702200-99715800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:99703400-99728200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr15:99704800-99711000	Enhancers	Rectal Smooth Muscle	rectum
25	chr15:99705000-99732400	Weak transcription	Fetal Kidney	kidney
26	chr15:99705400-99710600	Weak transcription	Fetal Lung	lung
27	chr15:99705400-99711000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:99705600-99715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:99706200-99710400	Enhancers	Psoas Muscle	Psoas
30	chr15:99706200-99715800	Genic enhancers	Fetal Muscle Leg	muscle
31	chr15:99706800-99711000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:99707000-99711600	Genic enhancers	Fetal Stomach	stomach
33	chr15:99707000-99711800	Enhancers	Colon Smooth Muscle	Colon
34	chr15:99707000-99715800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:99707400-99710800	Enhancers	Brain Substantia Nigra	brain
36	chr15:99707800-99712800	Weak transcription	HepG2	liver
37	chr15:99707800-99717200	Weak transcription	HUVEC	blood vessel
38	chr15:99708200-99711200	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr15:99708200-99711400	Enhancers	NHDF-Ad	bronchial
40	chr15:99708400-99711800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:99708600-99711200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:99708600-99715000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr15:99708600-99715800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:99708800-99710800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:99708800-99711200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:99709000-99710600	Enhancers	Brain Hippocampus Middle	brain
47	chr15:99709000-99710800	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr15:99709000-99711000	Enhancers	Right Ventricle	heart
49	chr15:99709000-99711600	Enhancers	Fetal Heart	heart
50	chr15:99709000-99715600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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