Variant report

Variant	rs11810706
Chromosome Location	chr1:176001826-176001827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175994034..175996077-chr1:176001633..176003490,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10218714	0.84[ASN][1000 genomes]
rs10494495	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10753112	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10753117	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10753118	0.84[ASN][1000 genomes]
rs10798425	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs10798434	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10798442	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10798444	0.84[ASN][1000 genomes]
rs10798445	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs10798446	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10913117	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10913118	0.95[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs10913120	0.86[ASN][1000 genomes]
rs10913124	0.92[ASN][1000 genomes]
rs10913131	0.85[ASN][1000 genomes]
rs10913132	0.83[ASN][1000 genomes]
rs10913135	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs10913137	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10913143	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10913144	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10913147	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12029090	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs12033847	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12049077	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12135395	0.97[EUR][1000 genomes]
rs12138008	0.95[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs12404596	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12723724	0.95[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs12729524	0.95[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs12735810	0.90[ASN][1000 genomes]
rs12741940	0.83[EUR][1000 genomes]
rs12756741	0.90[EUR][1000 genomes]
rs16849486	0.95[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs17354120	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2039230	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs2175177	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2457418	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs2481628	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs2481630	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs2481631	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs2481633	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs2481646	0.86[EUR][1000 genomes]
rs2481655	0.95[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs2487144	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs2502823	0.95[CEU][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs2502829	0.87[EUR][1000 genomes]
rs2502831	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs2502845	0.95[CEU][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap]
rs34973462	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934392	0.83[EUR][1000 genomes]
rs4409605	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs520661	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs617078	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs6660080	0.90[EUR][1000 genomes]
rs6665385	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs6678628	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6678812	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs6682194	0.96[EUR][1000 genomes]
rs6688898	0.84[ASN][1000 genomes]
rs6697860	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs679728	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs704829	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs704834	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs7515914	0.81[ASN][1000 genomes]
rs7517503	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7530719	0.90[EUR][1000 genomes]
rs7534058	0.84[ASN][1000 genomes]
rs7534948	0.81[ASN][1000 genomes]
rs7549160	0.86[CEU][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs791743	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs791751	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs791753	0.95[CEU][hapmap];0.84[JPT][hapmap]
rs813180	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs9425447	0.95[CEU][hapmap];0.85[JPT][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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv1835152	chr1:175996260-176012807	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11810706	FMO1	cis	parietal	SCAN
rs11810706	VAMP4	cis	parietal	SCAN
rs11810706	FMO2	cis	parietal	SCAN
rs11810706	EME2	trans	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:175973600-176003400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:175974000-176003000	Weak transcription	NH-A	brain
4	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:175975400-176003400	Weak transcription	NHLF	lung
6	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
7	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
8	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:175978200-176003600	Weak transcription	Small Intestine	intestine
11	chr1:175978200-176007400	Weak transcription	Brain Germinal Matrix	brain
12	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
13	chr1:175978400-176003000	Weak transcription	HSMM	muscle
14	chr1:175978400-176006800	Weak transcription	Fetal Brain Female	brain
15	chr1:175978400-176007000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:175978400-176007000	Weak transcription	Fetal Kidney	kidney
17	chr1:175978400-176014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:175978400-176014800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:175978600-176007000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:175978800-176003000	Weak transcription	A549	lung
23	chr1:175979200-176011800	Weak transcription	Brain Anterior Caudate	brain
24	chr1:175979400-176009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:175979400-176012200	Weak transcription	HepG2	liver
26	chr1:175979600-176010600	Weak transcription	Right Ventricle	heart
27	chr1:175979600-176012000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:175979800-176014400	Weak transcription	Brain Substantia Nigra	brain
30	chr1:175980200-176028000	Weak transcription	K562	blood
31	chr1:175981400-176009200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:175982000-176009800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:175982200-176003200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:175982200-176009400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:175982200-176009400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:175982200-176012200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:175982600-176003200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:175982800-176002800	Weak transcription	Hela-S3	cervix
39	chr1:175983400-176010600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:175985800-176005400	Weak transcription	GM12878-XiMat	blood
41	chr1:175988400-176009400	Weak transcription	Lung	lung
42	chr1:175989000-176003600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:175989000-176009400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:175989000-176009600	Weak transcription	Esophagus	oesophagus
45	chr1:175989400-176009400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:175989800-176002200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:175989800-176003600	Weak transcription	Fetal Stomach	stomach
48	chr1:175989800-176009400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:175989800-176009400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:175989800-176010600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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