Variant report

Variant	rs1080266
Chromosome Location	chr1:169176590-169176591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169171835..169174311-chr1:169174995..169177628,2	MCF-7	breast:

Extended variants
information (count: 136 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10800410	0.84[AFR][1000 genomes]
rs10800411	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs10800415	0.88[AFR][1000 genomes]
rs10800417	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10800419	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10800420	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10800429	0.84[CEU][hapmap]
rs1080267	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs10919082	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs10919084	0.82[AFR][1000 genomes]
rs10919086	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs10919090	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs10919095	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919106	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10919107	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10919108	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11802117	0.82[AFR][1000 genomes]
rs11802143	0.90[CHB][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11808938	0.90[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11809256	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12057602	0.90[CHB][hapmap]
rs12057856	0.82[AFR][1000 genomes]
rs12059281	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12065884	0.82[AFR][1000 genomes]
rs12066426	0.82[AFR][1000 genomes]
rs12067018	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs12067072	0.81[CHB][hapmap];0.84[AFR][1000 genomes]
rs12071277	0.81[AFR][1000 genomes]
rs12072226	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs12072953	0.82[AFR][1000 genomes]
rs12075832	0.81[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs12076469	0.81[CHB][hapmap]
rs12081283	0.90[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12083287	0.81[CHB][hapmap];0.84[AFR][1000 genomes]
rs12084549	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12084957	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12097151	0.90[CHB][hapmap]
rs12120493	0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs12121346	0.80[ASN][1000 genomes]
rs12121395	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12123168	0.90[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12124144	0.82[AFR][1000 genomes]
rs12124168	0.82[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs12125921	0.82[AFR][1000 genomes]
rs12125985	0.82[AFR][1000 genomes]
rs12126032	0.84[AFR][1000 genomes]
rs12126266	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12127305	0.84[AFR][1000 genomes]
rs12129979	1.00[CHB][hapmap]
rs12130764	0.84[AFR][1000 genomes]
rs12141151	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12141917	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12143965	0.81[CHB][hapmap]
rs12145969	0.90[CHB][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12354315	0.83[CEU][hapmap]
rs12562404	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs12564558	0.81[CHB][hapmap]
rs12564596	0.81[CHB][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs12724093	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12724802	0.81[CHB][hapmap]
rs12724863	0.83[AFR][1000 genomes]
rs12735503	0.80[AFR][1000 genomes]
rs12736110	0.81[AFR][1000 genomes]
rs12739920	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12740040	0.80[ASN][1000 genomes]
rs12741540	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12744184	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs12744341	0.81[CHB][hapmap]
rs12745997	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12747242	0.81[CHB][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs12751062	0.90[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12755385	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs12756799	0.81[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs1419323	0.83[CEU][hapmap]
rs16862093	0.88[CHB][hapmap]
rs16862095	0.90[CHB][hapmap]
rs2012763	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2032044	0.82[AFR][1000 genomes]
rs2300159	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2420012	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34250651	0.82[AFR][1000 genomes]
rs35631014	0.82[AFR][1000 genomes]
rs35774511	0.82[AFR][1000 genomes]
rs36079696	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3737681	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs3753297	0.83[CEU][hapmap];0.90[CHB][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3753300	0.90[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3766053	0.83[CEU][hapmap]
rs3766059	0.81[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs3766060	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap]
rs3766061	0.82[AFR][1000 genomes]
rs3766062	0.81[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs3766065	0.83[AFR][1000 genomes]
rs3766067	0.81[AFR][1000 genomes]
rs3766069	0.81[CHB][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs3766070	0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs3766071	0.84[AFR][1000 genomes]
rs3820053	0.81[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs3820055	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs3820056	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs4140540	0.81[CHB][hapmap]
rs4385775	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4445529	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4656181	0.90[CHB][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4656654	0.82[AFR][1000 genomes]
rs4656655	0.82[AFR][1000 genomes]
rs4656659	0.81[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs4656660	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs4656662	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4656666	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4656667	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6427180	0.90[CHB][hapmap]
rs6679084	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6688038	0.90[CHB][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6688139	0.90[CHB][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6695177	0.82[AFR][1000 genomes]
rs6695252	0.82[AFR][1000 genomes]
rs6701686	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6703463	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6704482	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs67485965	0.82[AFR][1000 genomes]
rs72700019	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7518554	0.81[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs7526721	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7541564	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs7541675	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs7547686	0.87[ASN][1000 genomes]
rs909929	0.81[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs909930	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes]
rs909931	0.83[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs932394	0.81[CHB][hapmap]
rs958581	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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 lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1080266	NME7	cis	Thyroid	GTEx
rs1080266	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1080266	NME7	cis	Nerve Tibial	GTEx
rs1080266	NME7	cis	Esophagus Muscularis	GTEx
rs1080266	NME7	cis	Artery Tibial	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169163600-169184000	Weak transcription	Ovary	ovary
3	chr1:169167800-169186800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:169168000-169183800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:169171600-169184000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:169172000-169176600	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:169172400-169183800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
9	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:169173200-169202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:169173600-169183800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:169176400-169176600	Enhancers	Aorta	Aorta
13	chr1:169176400-169177000	Enhancers	Rectal Smooth Muscle	rectum
14	chr1:169176400-169177800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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