Variant report

Variant	rs2420016
Chromosome Location	chr1:169261356-169261357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1028180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10442644	0.87[EUR][1000 genomes]
rs10753786	0.83[CHB][hapmap]
rs10800423	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10800447	0.83[CHB][hapmap]
rs1080268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919173	0.89[CHB][hapmap]
rs1208373	0.90[JPT][hapmap]
rs12116683	0.88[EUR][1000 genomes]
rs12117884	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118611	0.88[EUR][1000 genomes]
rs12118645	0.88[EUR][1000 genomes]
rs12121185	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12121346	0.83[EUR][1000 genomes]
rs12121994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124064	0.88[EUR][1000 genomes]
rs12125501	0.87[EUR][1000 genomes]
rs12129132	0.88[EUR][1000 genomes]
rs12129567	0.87[EUR][1000 genomes]
rs12142784	0.86[EUR][1000 genomes]
rs12143193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12145146	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12145226	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723917	0.88[EUR][1000 genomes]
rs12725912	0.95[ASN][1000 genomes]
rs12731520	0.87[EUR][1000 genomes]
rs12733001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12733037	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12733626	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735250	1.00[ASN][1000 genomes]
rs12738167	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739337	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12740040	0.83[EUR][1000 genomes]
rs12743588	0.88[EUR][1000 genomes]
rs12743782	1.00[ASN][1000 genomes]
rs12744362	0.87[EUR][1000 genomes]
rs12745541	0.94[ASN][1000 genomes]
rs12745978	0.88[EUR][1000 genomes]
rs12748624	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12751407	0.88[EUR][1000 genomes]
rs12751571	0.88[EUR][1000 genomes]
rs12751929	0.95[ASN][1000 genomes]
rs12752953	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12757669	0.97[ASN][1000 genomes]
rs1517745	0.89[CHB][hapmap]
rs1533518	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16828165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16862081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16862097	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16862176	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs16862180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16862217	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1883167	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2037249	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2066001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2152980	0.97[ASN][1000 genomes]
rs2271762	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2300158	0.83[CHB][hapmap]
rs2300160	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2420014	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2420015	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3213587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs34016668	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34248820	0.88[EUR][1000 genomes]
rs34408435	0.88[EUR][1000 genomes]
rs34469836	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34689938	0.97[ASN][1000 genomes]
rs34848249	1.00[ASN][1000 genomes]
rs34930817	0.95[ASN][1000 genomes]
rs35091267	0.86[EUR][1000 genomes]
rs35220898	0.86[EUR][1000 genomes]
rs35244822	0.97[ASN][1000 genomes]
rs35249110	0.85[EUR][1000 genomes]
rs35271076	0.86[EUR][1000 genomes]
rs35375125	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35393101	0.88[EUR][1000 genomes]
rs35406371	0.95[ASN][1000 genomes]
rs35435858	0.97[ASN][1000 genomes]
rs35448601	1.00[ASN][1000 genomes]
rs35493809	0.86[ASN][1000 genomes]
rs35539429	0.88[EUR][1000 genomes]
rs35639586	0.97[ASN][1000 genomes]
rs35680826	0.86[ASN][1000 genomes]
rs36023090	0.97[ASN][1000 genomes]
rs36040633	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36154866	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36179730	0.83[ASN][1000 genomes]
rs3753299	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766075	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766076	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3766078	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3862937	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4140538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4140539	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs41442344	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4589164	0.88[EUR][1000 genomes]
rs61808874	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61808916	0.88[EUR][1000 genomes]
rs61808940	0.88[EUR][1000 genomes]
rs6672589	0.89[CHB][hapmap]
rs6675220	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71523143	0.92[ASN][1000 genomes]
rs71635617	0.88[EUR][1000 genomes]
rs71635619	0.95[ASN][1000 genomes]
rs724048	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs72700059	0.88[EUR][1000 genomes]
rs7522781	0.91[EUR][1000 genomes]
rs929133	0.94[CHB][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1009170	chr1:169207940-169270995	Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv508637	chr1:169214920-169268078	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1004674	chr1:169233962-169271792	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2420016	NME7	cis	Artery Tibial	GTEx
rs2420016	NME7	cis	Thyroid	GTEx
rs2420016	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs2420016	NME7	cis	Nerve Tibial	GTEx
rs2420016	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169251400-169271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169253000-169264800	Weak transcription	Primary T cells from cord blood	blood
5	chr1:169253400-169270800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
7	chr1:169254000-169274800	Weak transcription	Ovary	ovary
8	chr1:169254400-169263600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:169254800-169268600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:169254800-169281000	Weak transcription	Dnd41	blood
11	chr1:169255800-169264800	Weak transcription	Aorta	Aorta
12	chr1:169256800-169271600	Weak transcription	Primary B cells from cord blood	blood
13	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:169257600-169268600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:169257800-169263400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:169258600-169271200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:169258600-169276400	Weak transcription	HSMM	muscle
20	chr1:169258800-169263600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:169258800-169264000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:169258800-169264200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:169258800-169274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:169258800-169277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:169259200-169278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:169259400-169274800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:169259400-169278600	Weak transcription	Adipose Nuclei	Adipose
28	chr1:169259600-169278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
30	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
31	chr1:169260600-169278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:169260800-169263400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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