Variant report

Variant	rs2273366
Chromosome Location	chr1:173724942-173724943
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	chr1:173718954..173722251-chr1:173724534..173727033,3	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10798290	0.90[CHB][hapmap]
rs10912651	0.84[CHB][hapmap]
rs10912670	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10912671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039524	0.85[CHB][hapmap]
rs12082131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12086229	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12561931	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12564699	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565915	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12566945	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1322774	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs16846439	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1951625	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs2067079	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2144708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2208850	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs2227588	0.90[CHB][hapmap]
rs2227612	0.90[CHB][hapmap]
rs2281486	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295366	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs28804123	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791020	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45467799	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4558043	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4652283	0.90[CHB][hapmap]
rs4652298	0.90[CHB][hapmap]
rs4652328	0.90[CHB][hapmap]
rs55633896	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55829688	0.94[ASN][1000 genomes]
rs56019876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56048122	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138893	0.91[ASN][1000 genomes]
rs56369162	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56928371	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57799150	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58287165	0.90[ASN][1000 genomes]
rs58825445	0.92[ASN][1000 genomes]
rs59858609	0.90[ASN][1000 genomes]
rs60264384	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61826805	0.91[ASN][1000 genomes]
rs61826806	0.91[ASN][1000 genomes]
rs61826809	0.91[ASN][1000 genomes]
rs61826810	0.91[ASN][1000 genomes]
rs61826812	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826813	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826856	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826857	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827860	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827863	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827865	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827867	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827870	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827876	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827877	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61827881	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827925	0.94[ASN][1000 genomes]
rs6413827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425251	0.90[CHB][hapmap]
rs6425253	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425261	0.94[ASN][1000 genomes]
rs6668702	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6673175	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674381	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681766	0.91[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6691001	0.94[ASN][1000 genomes]
rs6696680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7514556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7521884	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530546	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541082	0.90[CHB][hapmap]
rs7546048	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7548171	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425416	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425431	0.90[CHB][hapmap]
rs9425433	0.90[CHB][hapmap]
rs9425745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9425756	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs9660881	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv3598	chr1:173693027-173738687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2273366	DARS2	cis	parietal	SCAN
rs2273366	DARS2	cis	Muscle Skeletal	GTEx
rs2273366	TNN	cis	parietal	SCAN
rs2273366	RFWD2	cis	cerebellum	SCAN
rs2273366	SERPINC1	cis	multi-tissue	Pritchard
rs2273366	PRDX6	cis	parietal	SCAN
rs2273366	SLC9A11	cis	parietal	SCAN
rs2273366	DARS2	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173685400-173725000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:173686800-173725400	Weak transcription	Right Ventricle	heart
3	chr1:173695400-173726000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:173695800-173725000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:173695800-173726000	Weak transcription	Esophagus	oesophagus
6	chr1:173695800-173729800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:173696200-173726000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:173699600-173725800	Weak transcription	Fetal Kidney	kidney
9	chr1:173703400-173725000	Weak transcription	Colonic Mucosa	Colon
10	chr1:173703400-173725000	Weak transcription	Psoas Muscle	Psoas
11	chr1:173703400-173726000	Weak transcription	Aorta	Aorta
12	chr1:173703400-173726000	Weak transcription	Spleen	Spleen
13	chr1:173703400-173726000	Weak transcription	NHEK	skin
14	chr1:173703800-173728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:173704200-173725000	Weak transcription	NHLF	lung
16	chr1:173704400-173725000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:173704400-173725200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:173705800-173725400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:173710200-173726000	Weak transcription	Brain Germinal Matrix	brain
20	chr1:173713400-173731600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:173718600-173725000	Weak transcription	NHDF-Ad	bronchial
22	chr1:173718800-173725800	Weak transcription	A549	lung
23	chr1:173720000-173730000	Strong transcription	Primary B cells from cord blood	blood
24	chr1:173720000-173730600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:173720200-173727400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:173720200-173728000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr1:173720200-173729000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:173720200-173729000	Strong transcription	Dnd41	blood
29	chr1:173720200-173729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:173720200-173729800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:173720200-173730000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:173720200-173730200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:173720400-173726000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:173720400-173727000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:173720400-173729800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:173720600-173728000	Weak transcription	Stomach Mucosa	stomach
37	chr1:173720600-173728600	Strong transcription	Hela-S3	cervix
38	chr1:173720600-173729000	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:173720800-173727200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:173720800-173728800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:173720800-173728800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:173720800-173728800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:173720800-173729000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:173720800-173729000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr1:173720800-173729200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:173720800-173729400	Strong transcription	Primary T cells from cord blood	blood
47	chr1:173720800-173729600	Strong transcription	Adipose Nuclei	Adipose
48	chr1:173720800-173729800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:173720800-173729800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:173720800-173729800	Strong transcription	Fetal Thymus	thymus

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