Variant report

Variant	rs6587064
Chromosome Location	chr17:20207884-20207885
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1009082	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10438824	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11654025	0.81[CEU][hapmap]
rs11870147	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11871827	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11871945	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12935996	1.00[YRI][hapmap]
rs12937827	0.83[ASN][1000 genomes]
rs12941200	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12947950	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12948178	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12949485	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12952398	0.83[ASN][1000 genomes]
rs1373147	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1544421	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs1561974	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs17686622	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17686798	0.81[CEU][hapmap]
rs17686839	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs17759923	0.83[ASN][1000 genomes]
rs17759959	0.82[CEU][hapmap]
rs1812934	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs1985810	0.83[ASN][1000 genomes]
rs1992562	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2013441	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2013576	1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2034109	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2058971	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs2080673	0.83[ASN][1000 genomes]
rs2107566	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2120282	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2158473	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs2165897	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2189710	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2243732	0.83[ASN][1000 genomes]
rs2263175	0.83[ASN][1000 genomes]
rs2386429	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2386485	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs2526458	0.83[ASN][1000 genomes]
rs2526460	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs2526462	0.81[CEU][hapmap]
rs2526464	0.83[ASN][1000 genomes]
rs2526467	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2526468	0.96[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526469	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526470	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526471	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526472	0.83[ASN][1000 genomes]
rs2526473	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526474	0.83[ASN][1000 genomes]
rs2526475	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2526480	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2526483	0.83[ASN][1000 genomes]
rs2526484	0.83[CEU][hapmap];0.83[ASN][1000 genomes]
rs2526488	0.83[ASN][1000 genomes]
rs2526490	0.83[ASN][1000 genomes]
rs2526491	0.91[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2526492	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703772	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2703773	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703774	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703778	0.83[ASN][1000 genomes]
rs2703779	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703780	0.83[ASN][1000 genomes]
rs2703782	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703784	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703785	0.83[ASN][1000 genomes]
rs2703787	0.83[ASN][1000 genomes]
rs2703789	0.83[ASN][1000 genomes]
rs2703790	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703791	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703792	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703794	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703797	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703799	0.81[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2703801	0.84[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703802	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2703804	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703806	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703808	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2703810	0.83[ASN][1000 genomes]
rs2703811	0.91[EUR][1000 genomes]
rs2703813	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703815	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703816	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703817	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs2703818	0.83[ASN][1000 genomes]
rs2703820	0.83[ASN][1000 genomes]
rs2703821	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs34089239	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs34644796	0.83[ASN][1000 genomes]
rs34712254	0.83[ASN][1000 genomes]
rs35103332	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3850783	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs3850784	0.81[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs3850785	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs4588033	0.84[CEU][hapmap];0.83[ASN][1000 genomes]
rs4924808	0.81[CEU][hapmap]
rs4924809	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs4924810	0.81[CEU][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4925089	0.83[ASN][1000 genomes]
rs62066869	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62067558	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7207611	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7207817	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7223488	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8068720	0.82[CEU][hapmap]
rs8070401	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8071665	0.82[CEU][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8074047	0.83[ASN][1000 genomes]
rs8079701	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9325894	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs9892630	0.83[ASN][1000 genomes]
rs9896221	0.83[ASN][1000 genomes]
rs9896709	0.88[CEU][hapmap];0.83[ASN][1000 genomes]
rs9897328	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs9900166	0.83[ASN][1000 genomes]
rs9904928	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs9905493	0.82[CEU][hapmap];0.83[ASN][1000 genomes]
rs9915059	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv427993	chr17:20171398-20482061	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	nsv520772	chr17:20184501-20522444	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv521025	chr17:20198024-20514921	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6587064	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:20170400-20209600	Weak transcription	HMEC	breast
3	chr17:20185200-20209800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:20186000-20209400	Weak transcription	Spleen	Spleen
5	chr17:20186200-20209800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
7	chr17:20188200-20208400	Weak transcription	NHEK	skin
8	chr17:20188600-20209800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:20188600-20209800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr17:20190000-20208600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:20197800-20209800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:20200000-20209600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:20200800-20209200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:20200800-20209400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr17:20201000-20208000	Weak transcription	A549	lung
16	chr17:20201000-20220000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr17:20201200-20208600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:20201200-20209400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:20201400-20208000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:20201400-20208800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:20201400-20209800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:20201800-20209400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:20202000-20208000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr17:20202400-20209200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:20203800-20208200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr17:20203800-20208400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr17:20203800-20209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:20204000-20208200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:20204000-20208400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr17:20204000-20209800	Weak transcription	Fetal Intestine Small	intestine
31	chr17:20204200-20208600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:20204200-20209800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr17:20204200-20209800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr17:20204400-20209800	Weak transcription	Aorta	Aorta
35	chr17:20204400-20209800	Weak transcription	Fetal Intestine Large	intestine
36	chr17:20204400-20216800	Weak transcription	Gastric	stomach
37	chr17:20204600-20208400	Weak transcription	Adipose Nuclei	Adipose
38	chr17:20204600-20209800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr17:20204800-20209800	Weak transcription	HSMM	muscle
40	chr17:20204800-20209800	Weak transcription	HSMMtube	muscle
41	chr17:20204800-20212200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr17:20205400-20208000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:20205800-20208200	Weak transcription	Ovary	ovary
44	chr17:20205800-20208400	Weak transcription	Esophagus	oesophagus
45	chr17:20205800-20208600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:20205800-20210400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr17:20206000-20209600	Weak transcription	Osteobl	bone
48	chr17:20206600-20209400	Weak transcription	Brain Hippocampus Middle	brain
49	chr17:20206800-20208000	Weak transcription	Fetal Thymus	thymus
50	chr17:20206800-20208400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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