Variant report

Variant	rs2000321
Chromosome Location	chr1:169097463-169097464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169073905..169078334-chr1:169089982..169100946,16	MCF-7	breast:
2	chr1:169096516..169099051-chr1:169103916..169105981,2	K562	blood:
3	chr1:169092696..169095785-chr1:169096212..169101951,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1011638	1.00[JPT][hapmap]
rs1018832	0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10458388	0.83[AMR][1000 genomes]
rs10458394	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs10489417	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs10800429	1.00[JPT][hapmap]
rs10800431	1.00[JPT][hapmap]
rs10800432	1.00[JPT][hapmap]
rs10919062	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919070	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919071	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919074	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919085	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10919087	0.92[ASN][1000 genomes]
rs10919093	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10919127	1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap]
rs12021696	0.83[AMR][1000 genomes]
rs12025566	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12028197	0.83[AMR][1000 genomes]
rs12029800	1.00[JPT][hapmap]
rs12029857	0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12035622	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042082	1.00[JPT][hapmap]
rs12048188	0.80[AMR][1000 genomes]
rs12401966	0.80[AMR][1000 genomes]
rs12403181	0.80[AMR][1000 genomes]
rs12405725	0.85[JPT][hapmap]
rs12406341	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408636	0.83[AMR][1000 genomes]
rs12410241	0.83[AMR][1000 genomes]
rs12410387	0.80[AMR][1000 genomes]
rs12410456	0.80[AMR][1000 genomes]
rs12410548	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12568473	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17345156	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001155	0.80[AMR][1000 genomes]
rs2001156	0.80[AMR][1000 genomes]
rs2143290	0.81[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34323371	0.80[AMR][1000 genomes]
rs3766074	0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72706963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72706975	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413522	1.00[JPT][hapmap]
rs7556463	1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2000321	ATP1B1	cis	Brain Pons	GTEx
rs2000321	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs2000321	MPZL1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169081000-169098200	Weak transcription	Small Intestine	intestine
3	chr1:169082200-169097600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:169084200-169099200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:169085400-169097600	Weak transcription	Fetal Brain Male	brain
6	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:169085800-169100000	Weak transcription	Thymus	Thymus
8	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
10	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:169086400-169100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:169089600-169101600	Genic enhancers	A549	lung
15	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:169090000-169098200	Weak transcription	NHDF-Ad	bronchial
17	chr1:169090000-169098400	Weak transcription	HSMMtube	muscle
18	chr1:169090000-169103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:169090400-169103200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:169090600-169098400	Strong transcription	HSMM	muscle
21	chr1:169091000-169102200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:169091000-169102200	Strong transcription	HepG2	liver
23	chr1:169091000-169102800	Strong transcription	Hela-S3	cervix
24	chr1:169091200-169124600	Weak transcription	NHLF	lung
25	chr1:169091400-169098400	Weak transcription	Aorta	Aorta
26	chr1:169091400-169102200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:169091400-169103200	Strong transcription	Liver	Liver
28	chr1:169091400-169103400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:169091600-169097800	Weak transcription	Psoas Muscle	Psoas
30	chr1:169091600-169101200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:169091600-169102000	Weak transcription	Pancreas	Pancrea
32	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
33	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:169091600-169120600	Weak transcription	Lung	lung
35	chr1:169091800-169104200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
37	chr1:169092200-169098400	Strong transcription	HMEC	breast
38	chr1:169092200-169102400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:169092400-169106200	Weak transcription	Gastric	stomach
40	chr1:169092600-169103600	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:169092800-169098400	Strong transcription	Left Ventricle	heart
42	chr1:169093200-169100800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:169093200-169103200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:169093400-169097800	Strong transcription	HUVEC	blood vessel
45	chr1:169093400-169099400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr1:169093400-169099400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:169093400-169102000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:169093400-169102000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:169093400-169102800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:169093600-169102200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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