Variant report

Variant	rs10494234
Chromosome Location	chr1:120513447-120513448
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	chr1:120511011..120512571-chr1:120512648..120514859,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1043964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494233	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493693	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024486	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024487	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024508	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024519	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024521	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024536	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024584	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024593	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17258606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795666	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56342935	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59024536	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115387	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115388	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115390	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115392	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115396	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115509	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117505	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117563	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117565	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117567	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117568	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74117570	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412780	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7527186	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1816057	chr1:120469050-120697156	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv1818054	chr1:120469050-120697156	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv1844863	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv1850218	chr1:120469050-120697156	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv427730	chr1:120469050-120697156	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10494234	TBC1D30	trans	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120468600-120532800	Weak transcription	Stomach Mucosa	stomach
2	chr1:120490000-120514400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:120490000-120517600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:120490200-120521000	Strong transcription	Primary B cells from cord blood	blood
5	chr1:120490800-120515000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:120491200-120538800	Weak transcription	Fetal Brain Male	brain
7	chr1:120499400-120514600	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:120500200-120515400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:120504600-120515000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:120504600-120517600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:120504800-120514000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:120505200-120515200	Strong transcription	Dnd41	blood
13	chr1:120505400-120514600	Strong transcription	Thymus	Thymus
14	chr1:120505400-120514800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:120505600-120514600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:120505600-120514600	Strong transcription	Primary hematopoietic stem cells	blood
17	chr1:120507200-120514200	Strong transcription	Fetal Kidney	kidney
18	chr1:120508000-120514400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr1:120508000-120515800	Strong transcription	Fetal Stomach	stomach
20	chr1:120508000-120517800	Weak transcription	Psoas Muscle	Psoas
21	chr1:120508200-120514600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr1:120508400-120515600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:120508400-120518600	Weak transcription	Fetal Brain Female	brain
24	chr1:120508600-120529800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:120508800-120517800	Weak transcription	Brain Angular Gyrus	brain
26	chr1:120508800-120524600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:120509000-120514000	Strong transcription	NH-A	brain
28	chr1:120509000-120516000	Weak transcription	Small Intestine	intestine
29	chr1:120509000-120533000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:120509200-120514400	Strong transcription	NHLF	lung
31	chr1:120509200-120515000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:120509400-120514600	Strong transcription	Fetal Lung	lung
33	chr1:120509600-120514600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:120509600-120515400	Weak transcription	Brain Substantia Nigra	brain
35	chr1:120509600-120520600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:120509600-120520600	Weak transcription	Right Ventricle	heart
37	chr1:120509800-120557600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:120510200-120514000	Strong transcription	Pancreas	Pancrea
39	chr1:120510200-120517600	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:120510200-120519800	Weak transcription	Fetal Heart	heart
41	chr1:120510200-120529600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:120510200-120532800	Weak transcription	Brain Anterior Caudate	brain
43	chr1:120510200-120538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:120510200-120552200	Weak transcription	HUVEC	blood vessel
45	chr1:120510400-120529800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:120510600-120516200	Strong transcription	HSMMtube	muscle
47	chr1:120510600-120516800	Weak transcription	A549	lung
48	chr1:120510600-120527400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:120510600-120528400	Weak transcription	Hela-S3	cervix
50	chr1:120510800-120514000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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