Variant report

Variant	rs2602016
Chromosome Location	chr15:99715352-99715353
allele	A/G
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	BHLHE40	chr15:99715191-99715536	K562	blood:	n/a	n/a
2	TEAD4	chr15:99715250-99715516	K562	blood:	n/a	n/a
3	TAL1	chr15:99715262-99715448	K562	blood:	n/a	n/a
4	MAX	chr15:99715256-99715415	K562	blood:	n/a	n/a
5	RCOR1	chr15:99715243-99715567	K562	blood:	n/a	n/a
6	POLR2A	chr15:99715143-99715459	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
TTC23	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10902539	0.94[AMR][1000 genomes]
rs12907394	1.00[ASW][hapmap]
rs1670213	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1670216	0.95[CEU][hapmap];0.86[AMR][1000 genomes]
rs1670224	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1670230	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs1703762	0.95[CEU][hapmap];0.89[AMR][1000 genomes]
rs1703763	0.86[AMR][1000 genomes]
rs1703766	0.95[CEU][hapmap];0.86[AMR][1000 genomes]
rs1703771	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs187755	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs260114	0.95[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602018	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2602020	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2602022	0.84[AMR][1000 genomes]
rs2602025	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2602026	0.94[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2602031	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602035	0.91[AMR][1000 genomes]
rs2602038	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623185	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2623188	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2623189	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2623190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2924346	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3210942	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes]
rs3743248	0.81[AMR][1000 genomes]
rs4573918	0.81[AMR][1000 genomes]
rs4602019	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4965217	0.86[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6598224	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6598225	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7163625	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
rs2602016	TTC23	cis	multi-tissue	Pritchard
rs2602016	TTC23	cis	cerebellum	SCAN
rs2602016	SYNM	cis	cerebellum	SCAN
rs2602016	TTC23	cis	parietal	SCAN
rs2602016	SYNM	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:99692000-99717000	Weak transcription	HSMM	muscle
5	chr15:99694800-99721200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr15:99694800-99732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:99694800-99732600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:99695200-99721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:99695200-99721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:99695200-99732400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:99697000-99716800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
13	chr15:99699400-99731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:99700200-99731200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:99700400-99730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:99702200-99715800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr15:99703400-99728200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:99705000-99732400	Weak transcription	Fetal Kidney	kidney
19	chr15:99705600-99715400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:99706200-99715800	Genic enhancers	Fetal Muscle Leg	muscle
21	chr15:99707000-99715800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:99707800-99717200	Weak transcription	HUVEC	blood vessel
23	chr15:99708600-99715800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:99709000-99715600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:99709400-99715400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:99709400-99732600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:99709600-99715800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:99709600-99731400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:99709600-99732600	Weak transcription	GM12878-XiMat	blood
30	chr15:99709800-99732600	Weak transcription	Spleen	Spleen
31	chr15:99710000-99719600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:99710000-99721000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:99710200-99724000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:99710400-99732400	Weak transcription	Fetal Brain Female	brain
35	chr15:99710800-99715400	Strong transcription	Dnd41	blood
36	chr15:99711000-99715600	Strong transcription	Fetal Intestine Large	intestine
37	chr15:99711200-99715600	Weak transcription	Right Ventricle	heart
38	chr15:99711200-99715800	Strong transcription	Adipose Nuclei	Adipose
39	chr15:99711200-99716000	Strong transcription	Liver	Liver
40	chr15:99711200-99720000	Weak transcription	Brain Anterior Caudate	brain
41	chr15:99711400-99715800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:99711400-99717000	Weak transcription	NHDF-Ad	bronchial
43	chr15:99711400-99730800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:99711600-99717600	Weak transcription	HMEC	breast
45	chr15:99711600-99721400	Weak transcription	NHLF	lung
46	chr15:99711600-99725000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:99711600-99738600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr15:99711800-99732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:99712200-99717200	Strong transcription	Fetal Intestine Small	intestine
50	chr15:99712400-99715800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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