Variant report

Variant	rs8009997
Chromosome Location	chr14:55421911-55421912
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55420812..55423243-chr14:55429568..55431730,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1002054	0.87[JPT][hapmap]
rs10129318	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10129802	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10136972	0.80[ASN][1000 genomes]
rs10137071	0.80[ASN][1000 genomes]
rs10139354	0.84[ASN][1000 genomes]
rs10140164	0.85[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs10145268	0.87[JPT][hapmap]
rs10148100	0.84[ASN][1000 genomes]
rs10150110	0.94[ASN][1000 genomes]
rs1107960	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs11158028	0.86[JPT][hapmap]
rs11158029	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11621165	0.86[JPT][hapmap]
rs11846514	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11846809	0.88[ASN][1000 genomes]
rs1187876	0.85[JPT][hapmap]
rs1187877	0.87[JPT][hapmap]
rs1187883	0.93[JPT][hapmap]
rs1201378	0.87[JPT][hapmap]
rs1209087	0.87[JPT][hapmap]
rs12147796	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13379159	0.87[JPT][hapmap]
rs17128120	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17832269	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832311	0.87[JPT][hapmap]
rs2149482	0.80[ASN][1000 genomes]
rs2183085	0.88[ASN][1000 genomes]
rs2251366	0.87[JPT][hapmap]
rs2840268	0.88[ASN][1000 genomes]
rs28446981	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28481699	0.92[ASN][1000 genomes]
rs28693954	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2878172	0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs2878174	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34988865	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3742564	0.87[JPT][hapmap]
rs3759664	0.86[JPT][hapmap]
rs3759665	0.80[ASN][1000 genomes]
rs3783643	0.96[ASN][1000 genomes]
rs3783644	0.98[ASN][1000 genomes]
rs3783645	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3783646	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4325453	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4335711	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56164809	0.88[ASN][1000 genomes]
rs56206440	0.94[ASN][1000 genomes]
rs56335168	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57622454	0.81[ASN][1000 genomes]
rs57667631	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57922954	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58055971	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59323730	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60028867	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61224609	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6572992	0.86[ASN][1000 genomes]
rs6572993	0.98[ASN][1000 genomes]
rs6572994	0.99[ASN][1000 genomes]
rs6572997	0.84[ASN][1000 genomes]
rs6572999	0.87[JPT][hapmap]
rs66769866	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66820631	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67395322	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67571433	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68065548	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7144652	0.87[JPT][hapmap]
rs7146285	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7147286	0.80[CEU][hapmap]
rs7151670	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7152033	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7153937	0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7157085	0.94[ASN][1000 genomes]
rs7159232	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7159933	0.93[ASN][1000 genomes]
rs7159953	0.83[ASN][1000 genomes]
rs72715573	0.94[ASN][1000 genomes]
rs8004402	0.88[ASN][1000 genomes]
rs8005399	0.87[JPT][hapmap]
rs8005471	0.96[ASN][1000 genomes]
rs8006977	0.94[ASN][1000 genomes]
rs8007267	0.86[JPT][hapmap]
rs8008150	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8011446	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8012152	0.88[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8012156	0.87[JPT][hapmap]
rs8013521	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8015172	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018800	0.94[ASN][1000 genomes]
rs8019220	0.94[ASN][1000 genomes]
rs8019390	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8020545	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs8021303	0.99[ASN][1000 genomes]
rs8021370	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8022049	0.94[ASW][hapmap];0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8022453	0.86[JPT][hapmap]
rs8023187	0.83[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9285583	0.99[ASN][1000 genomes]
rs9323275	0.87[ASN][1000 genomes]
rs943914	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9805952	0.92[ASN][1000 genomes]
rs9806049	0.81[JPT][hapmap]

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	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1038242	chr14:55398559-55444839	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3378942	chr14:55412251-55440744	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8009997	ATG14	cis	parietal	SCAN
rs8009997	RPL13AP3	cis	cerebellum	SCAN
rs8009997	FBXO34	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55394200-55443000	Weak transcription	HSMMtube	muscle
2	chr14:55394400-55428800	Weak transcription	HSMM	muscle
3	chr14:55395200-55422800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr14:55402000-55427600	Weak transcription	Fetal Brain Female	brain
5	chr14:55403000-55449000	Weak transcription	Gastric	stomach
6	chr14:55403200-55442600	Weak transcription	NHEK	skin
7	chr14:55403200-55442800	Weak transcription	NHDF-Ad	bronchial
8	chr14:55403600-55423800	Weak transcription	K562	blood
9	chr14:55403600-55428600	Weak transcription	HUVEC	blood vessel
10	chr14:55404400-55427600	Weak transcription	Primary T cells from cord blood	blood
11	chr14:55407400-55442800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr14:55407600-55427800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr14:55408000-55423200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr14:55408400-55423600	Weak transcription	GM12878-XiMat	blood
15	chr14:55408400-55429200	Weak transcription	Fetal Lung	lung
16	chr14:55409800-55423200	Weak transcription	Primary B cells from cord blood	blood
17	chr14:55410000-55427800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr14:55411000-55477000	Weak transcription	Left Ventricle	heart
19	chr14:55412200-55427600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr14:55412400-55453400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr14:55412600-55433600	Weak transcription	HepG2	liver
22	chr14:55413600-55429400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr14:55414000-55433800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr14:55414400-55423200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr14:55414400-55429800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr14:55415200-55450000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr14:55415400-55427600	Weak transcription	Fetal Intestine Large	intestine
28	chr14:55415400-55443000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr14:55415600-55423200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr14:55415600-55423200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr14:55415600-55423400	Weak transcription	Fetal Muscle Leg	muscle
32	chr14:55415600-55424800	Weak transcription	Thymus	Thymus
33	chr14:55415600-55425200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr14:55415600-55427600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:55415600-55427800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr14:55415600-55428800	Weak transcription	Hela-S3	cervix
37	chr14:55415800-55423200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:55415800-55427600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr14:55415800-55427600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr14:55415800-55427600	Weak transcription	A549	lung
41	chr14:55416000-55422600	Weak transcription	Fetal Stomach	stomach
42	chr14:55416000-55423000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr14:55416000-55423200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr14:55416000-55427400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr14:55416000-55442600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr14:55416200-55422600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr14:55416200-55423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:55416200-55425400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:55417400-55428800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr14:55418600-55492200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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