Variant report

Variant	rs1200164
Chromosome Location	chr1:169126895-169126896
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169124501..169127273-chr1:169133900..169136216,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10081960	0.80[ASN][1000 genomes]
rs1018831	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10732287	0.82[JPT][hapmap]
rs10753785	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800414	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800424	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10800425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10800435	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919105	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10919124	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1200076	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200077	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs1200083	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200085	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1200159	0.85[AFR][1000 genomes]
rs1200161	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1208370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208371	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208375	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12086665	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs12137282	0.80[ASN][1000 genomes]
rs12138150	0.80[ASN][1000 genomes]
rs12752748	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1400839	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1591733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16861990	0.82[JPT][hapmap]
rs17345107	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs17349222	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1829287	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1856303	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2037250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066000	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2152979	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2179490	0.80[ASN][1000 genomes]
rs2211017	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2420008	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs3766057	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4264046	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4454599	0.86[ASN][1000 genomes]
rs4656178	0.80[ASN][1000 genomes]
rs61803315	0.80[ASN][1000 genomes]
rs61803316	0.80[ASN][1000 genomes]
rs6662237	0.86[ASN][1000 genomes]
rs6691226	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7522760	0.80[ASN][1000 genomes]
rs7533257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7542713	0.80[ASN][1000 genomes]
rs7552323	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1200164	NME7	cis	Esophagus Muscularis	GTEx
rs1200164	NME7	cis	Stomach	GTEx
rs1200164	NME7	cis	lung	GTEx
rs1200164	NME7	cis	Artery Tibial	GTEx
rs1200164	NME7	cis	Nerve Tibial	GTEx
rs1200164	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1200164	NME7	cis	Thyroid	GTEx
rs1200164	NME7	cis	Artery Aorta	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
2	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
3	chr1:169097000-169130000	Weak transcription	Ovary	ovary
4	chr1:169100800-169141400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:169101000-169137000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:169103400-169130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:169104800-169142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:169115800-169130400	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:169116200-169130200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:169116400-169139400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:169118000-169137000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:169118200-169130400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:169118600-169130000	Weak transcription	Liver	Liver
14	chr1:169120400-169130200	Weak transcription	A549	lung
15	chr1:169121000-169129200	Weak transcription	Lung	lung
16	chr1:169121000-169137000	Weak transcription	Psoas Muscle	Psoas
17	chr1:169121000-169140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:169121200-169141200	Weak transcription	Left Ventricle	heart
19	chr1:169121800-169143000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:169122600-169130200	Weak transcription	NHEK	skin
21	chr1:169122800-169136400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:169124200-169127600	Enhancers	Fetal Intestine Large	intestine
23	chr1:169124400-169128000	Enhancers	Fetal Intestine Small	intestine
24	chr1:169124600-169130200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:169124800-169130800	Weak transcription	Gastric	stomach
26	chr1:169124800-169138800	Weak transcription	Primary B cells from cord blood	blood
27	chr1:169125400-169130000	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:169125400-169130200	Weak transcription	Right Ventricle	heart
29	chr1:169125400-169131200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:169126000-169127000	Enhancers	Stomach Mucosa	stomach
31	chr1:169126200-169127200	Enhancers	Duodenum Mucosa	Duodenum
32	chr1:169126400-169127200	Enhancers	Small Intestine	intestine
33	chr1:169126600-169127000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:169126600-169127400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:169126600-169128000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:169126800-169127000	Weak transcription	Right Atrium	heart
37	chr1:169126800-169130000	Weak transcription	Fetal Heart	heart

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