Variant report

Variant	rs12517207
Chromosome Location	chr5:59993268-59993269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:59978724..59981449-chr5:59990551..59993454,2	K562	blood:
2	chr5:59933171..59934818-chr5:59991480..59994360,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10043291	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10054744	0.81[ASN][1000 genomes]
rs10058456	1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10062240	0.88[CEU][hapmap]
rs10069929	0.81[ASN][1000 genomes]
rs10440618	0.81[ASN][1000 genomes]
rs10471493	0.81[ASN][1000 genomes]
rs10939858	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10939860	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs10939862	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1117674	0.81[ASN][1000 genomes]
rs1117675	0.81[ASN][1000 genomes]
rs1117677	0.81[ASN][1000 genomes]
rs11740327	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs11741754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11948543	0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs11954496	0.82[ASN][1000 genomes]
rs11955398	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11959922	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs12186391	0.99[ASN][1000 genomes]
rs12514253	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12515025	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs12517174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12522801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12651791	0.80[ASN][1000 genomes]
rs12655977	0.81[ASN][1000 genomes]
rs1379114	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs1379115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1379116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1444237	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs1456742	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1456743	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1460958	1.00[ASW][hapmap];0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap]
rs17387940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807017	0.84[CEU][hapmap]
rs1824120	1.00[ASN][1000 genomes]
rs1870014	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs1960479	0.81[ASN][1000 genomes]
rs1992612	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2061250	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs206789	0.82[CHD][hapmap]
rs2085409	0.87[ASN][1000 genomes]
rs2085410	0.82[ASN][1000 genomes]
rs2085411	0.84[ASN][1000 genomes]
rs2085413	0.84[ASN][1000 genomes]
rs2100584	0.87[ASN][1000 genomes]
rs2198865	0.81[EUR][1000 genomes]
rs2409792	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs2409794	0.86[ASN][1000 genomes]
rs286153	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs286154	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs286158	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs2898288	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3857236	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs3899221	0.81[ASN][1000 genomes]
rs4277863	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4398599	0.81[ASN][1000 genomes]
rs4400080	0.81[ASN][1000 genomes]
rs4447941	0.84[ASN][1000 genomes]
rs4524466	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4577661	0.81[ASN][1000 genomes]
rs4700384	0.81[ASN][1000 genomes]
rs55854817	0.98[ASN][1000 genomes]
rs56726435	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59155887	0.82[EUR][1000 genomes]
rs6449487	0.80[ASN][1000 genomes]
rs6449490	0.82[ASN][1000 genomes]
rs6449491	0.82[ASN][1000 genomes]
rs6449493	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6874699	0.88[CEU][hapmap]
rs6882727	0.82[ASN][1000 genomes]
rs6887434	0.81[ASN][1000 genomes]
rs755077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7701708	0.84[ASN][1000 genomes]
rs7704338	0.85[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7707698	0.99[ASN][1000 genomes]
rs7709056	0.81[EUR][1000 genomes]
rs7719611	0.85[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7720233	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7730342	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs7736518	0.94[ASN][1000 genomes]
rs930864	0.85[ASN][1000 genomes]
rs9654363	0.81[ASN][1000 genomes]
rs9686489	0.99[ASN][1000 genomes]
rs9942410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

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	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers 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
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12517207	ELOVL7	cis	parietal	SCAN
rs12517207	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs12517207	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs12517207	DEPDC1B	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59969600-59994800	Weak transcription	Fetal Lung	lung
2	chr5:59971000-59993800	Weak transcription	NHLF	lung
3	chr5:59971000-59994000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:59971000-59994200	Weak transcription	NH-A	brain
5	chr5:59974200-59994200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr5:59974400-59993600	Weak transcription	Hela-S3	cervix
7	chr5:59977200-59994800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:59980200-59995200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:59981800-59994200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:59982400-59993600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:59982600-59994800	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:59982800-59993800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:59982800-59994800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:59982800-59994800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:59983000-59994000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:59983000-59994000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:59983000-59994000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:59983000-59994200	Weak transcription	Thymus	Thymus
19	chr5:59983000-59994600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:59983000-59994800	Weak transcription	Fetal Thymus	thymus
21	chr5:59983000-59994800	Weak transcription	HSMM	muscle
22	chr5:59983200-59993800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:59983200-59993800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:59984600-59994000	Weak transcription	Fetal Heart	heart
25	chr5:59984600-59994800	Weak transcription	Fetal Intestine Small	intestine
26	chr5:59986800-59994000	Weak transcription	Osteobl	bone
27	chr5:59991400-59993400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:59991400-59993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:59991400-59993400	Weak transcription	A549	lung
30	chr5:59991400-59994000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:59991400-59994000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:59991400-59994200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:59991400-59994200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr5:59991400-59994800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:59991400-59994800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:59991400-59995000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:59991400-59995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:59991400-59995200	Weak transcription	Pancreas	Pancrea
39	chr5:59991600-59994000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:59991600-59994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:59991600-59994400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:59991600-59994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:59991800-59995200	Weak transcription	Psoas Muscle	Psoas
44	chr5:59992000-59993400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:59992400-59994200	Enhancers	HepG2	liver
46	chr5:59992400-59994800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:59992600-59994800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:59992600-59996600	Active TSS	GM12878-XiMat	blood
49	chr5:59992800-59993400	Enhancers	NHEK	skin
50	chr5:59993000-59994200	Enhancers	HUES64 Cell Line	embryonic stem cell

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