Variant report

Variant	rs5634
Chromosome Location	chr12:120762837-120762838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120727172..120733111-chr12:120749358..120767260,47	MCF-7	breast:
2	chr12:120761038..120763452-chr12:120881221..120883807,2	K562	blood:
3	chr12:120761708..120763403-chr12:120867083..120868587,2	MCF-7	breast:
4	chr12:120761819..120763866-chr12:120791381..120794631,4	K562	blood:
5	chr12:120758856..120760738-chr12:120761822..120763461,2	MCF-7	breast:
6	chr12:120762089..120763810-chr12:120905605..120907503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000111786	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12299143	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12423303	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12424233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12424555	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12426900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12427069	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12427095	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950044	1.00[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16950047	0.82[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16950058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16950061	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16950065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16950101	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2238158	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2238161	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2464296	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2522140	0.88[EUR][1000 genomes]
rs2701643	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905543	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3847967	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs3847968	0.82[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3847969	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3898618	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56237802	0.86[ASN][1000 genomes]
rs56733641	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57141366	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57279831	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57384430	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58232894	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59447311	0.92[EUR][1000 genomes]
rs59768240	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60176939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60731947	0.93[EUR][1000 genomes]
rs61140476	0.83[EUR][1000 genomes]
rs61592165	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61665022	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61748115	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960401	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977875	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9657936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657937	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9657941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657948	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv1035698	chr12:120645330-120777580	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
3	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers 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	436 gene(s)	inside rSNPs	diseases
4	nsv560435	chr12:120695141-120769657	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases
5	nsv899556	chr12:120695141-120779931	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	433 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5634	SIRT4	cis	lymphoblastoid	seeQTL
rs5634	SIRT4	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120755400-120763200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:120755400-120763600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:120756000-120763200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:120756200-120763200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr12:120756200-120763200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:120756200-120763200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:120756200-120763200	Weak transcription	GM12878-XiMat	blood
8	chr12:120756200-120763400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:120757000-120763200	Weak transcription	Thymus	Thymus
10	chr12:120759400-120763200	Weak transcription	K562	blood
11	chr12:120760000-120763400	Weak transcription	Fetal Kidney	kidney
12	chr12:120760200-120763200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:120760200-120763200	Weak transcription	Stomach Mucosa	stomach
14	chr12:120760200-120763400	Weak transcription	Colonic Mucosa	Colon
15	chr12:120760400-120763400	Weak transcription	A549	lung
16	chr12:120760600-120763200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:120761200-120765800	Active TSS	Pancreas	Pancrea
18	chr12:120761400-120765600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr12:120761800-120763600	Weak transcription	Spleen	Spleen
20	chr12:120762400-120763200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:120762400-120763400	Enhancers	Liver	Liver
22	chr12:120762400-120763400	Enhancers	Fetal Intestine Small	intestine
23	chr12:120762600-120763400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:120762600-120763400	Enhancers	Fetal Intestine Large	intestine
25	chr12:120762800-120763000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:120762800-120763000	Enhancers	Gastric	stomach
27	chr12:120762800-120763200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:120762800-120763200	Enhancers	Fetal Thymus	thymus
29	chr12:120762800-120763400	Enhancers	Fetal Muscle Trunk	muscle
30	chr12:120762800-120763400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr12:120762800-120763400	Enhancers	Dnd41	blood
32	chr12:120762800-120763400	Flanking Active TSS	HepG2	liver
33	chr12:120762800-120763800	Active TSS	Skeletal Muscle Male	skeletal muscle

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