Variant report

Variant	rs2602018
Chromosome Location	chr15:99727632-99727633
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10902539	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1238348	0.82[CHB][hapmap]
rs12907394	0.82[CHD][hapmap]
rs12915090	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1670213	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1670216	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1670224	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1670230	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes]
rs1703761	0.90[CHD][hapmap]
rs1703762	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1703763	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1703765	0.90[CHB][hapmap]
rs1703766	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1703771	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs187755	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs260087	0.81[AMR][1000 genomes]
rs260114	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2602015	0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2602016	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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602021	1.00[ASW][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs2602022	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2602025	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602031	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2602035	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602036	1.00[ASW][hapmap];0.82[CHB][hapmap]
rs2602038	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2623181	0.86[AFR][1000 genomes]
rs2623184	1.00[ASW][hapmap]
rs2623185	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2623188	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623189	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623190	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2623191	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2623193	0.93[AFR][1000 genomes]
rs2924346	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3210942	1.00[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes]
rs4602019	0.81[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs4965217	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6598224	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6598225	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163625	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7183226	1.00[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2602018	TTC23	cis	cerebellum	SCAN
rs2602018	SYNM	cis	cerebellum	SCAN
rs2602018	TTC23	cis	parietal	SCAN
rs2602018	SYNM	cis	parietal	SCAN
rs2602018	TTC23	cis	multi-tissue	Pritchard
rs2602018	NR2F2	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99694800-99732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:99694800-99732600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:99695200-99732400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
6	chr15:99699400-99731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:99700200-99731200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:99700400-99730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:99703400-99728200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:99705000-99732400	Weak transcription	Fetal Kidney	kidney
11	chr15:99709400-99732600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:99709600-99731400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:99709600-99732600	Weak transcription	GM12878-XiMat	blood
14	chr15:99709800-99732600	Weak transcription	Spleen	Spleen
15	chr15:99710400-99732400	Weak transcription	Fetal Brain Female	brain
16	chr15:99711400-99730800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:99711600-99738600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:99711800-99732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:99712800-99731600	Weak transcription	Colonic Mucosa	Colon
20	chr15:99715400-99731400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:99715600-99732600	Weak transcription	Pancreas	Pancrea
22	chr15:99715600-99732600	Weak transcription	NHEK	skin
23	chr15:99715600-99738600	Weak transcription	Hela-S3	cervix
24	chr15:99716000-99732400	Weak transcription	Esophagus	oesophagus
25	chr15:99717400-99761000	Weak transcription	Gastric	stomach
26	chr15:99717800-99758000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr15:99718200-99749200	Weak transcription	HUVEC	blood vessel
28	chr15:99719400-99732800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:99720000-99732400	Weak transcription	Ovary	ovary
30	chr15:99720200-99732200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:99721200-99738600	Weak transcription	HSMMtube	muscle
32	chr15:99721200-99758400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:99721400-99732400	Weak transcription	A549	lung
34	chr15:99721600-99730800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:99721600-99735600	Weak transcription	Dnd41	blood
36	chr15:99721800-99742400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:99722000-99730200	Weak transcription	Left Ventricle	heart
38	chr15:99722000-99758400	Weak transcription	Right Ventricle	heart
39	chr15:99722200-99731200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:99722200-99731400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:99722200-99731400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr15:99722200-99732400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:99722200-99732600	Weak transcription	Placenta	Placenta
44	chr15:99722200-99739800	Weak transcription	NHLF	lung
45	chr15:99722400-99752200	Weak transcription	Osteobl	bone
46	chr15:99722600-99757600	Weak transcription	Psoas Muscle	Psoas
47	chr15:99722800-99731000	Weak transcription	Fetal Lung	lung
48	chr15:99722800-99731400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:99722800-99731400	Weak transcription	HepG2	liver
50	chr15:99722800-99732600	Weak transcription	Rectal Smooth Muscle	rectum

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