Variant report

Variant	rs6446725
Chromosome Location	chr4:3173834-3173835
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	chr4:3173185..3175409-chr4:3176697..3178512,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10006373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012793	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021254	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10034669	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10155264	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10488840	1.00[EUR][1000 genomes]
rs16844026	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16844028	1.00[EUR][1000 genomes]
rs2003530	0.97[EUR][1000 genomes]
rs2005787	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28436280	0.92[EUR][1000 genomes]
rs28507598	0.83[EUR][1000 genomes]
rs28643391	0.99[EUR][1000 genomes]
rs28834148	1.00[ASN][1000 genomes]
rs3025825	0.99[EUR][1000 genomes]
rs362269	0.82[EUR][1000 genomes]
rs362274	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs362276	0.91[EUR][1000 genomes]
rs362278	1.00[EUR][1000 genomes]
rs362303	0.85[CEU][hapmap]
rs362305	0.80[EUR][1000 genomes]
rs362310	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs362323	0.99[EUR][1000 genomes]
rs362325	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs362338	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs363067	1.00[ASN][1000 genomes]
rs363068	1.00[ASN][1000 genomes]
rs363070	1.00[ASN][1000 genomes]
rs363082	1.00[ASN][1000 genomes]
rs363090	0.93[EUR][1000 genomes]
rs363091	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs363093	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363094	0.97[EUR][1000 genomes]
rs363095	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs363097	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363098	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363100	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363101	0.95[EUR][1000 genomes]
rs363106	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs363124	0.93[EUR][1000 genomes]
rs363125	0.93[EUR][1000 genomes]
rs363128	1.00[EUR][1000 genomes]
rs363141	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59147561	1.00[ASN][1000 genomes]
rs59588638	0.85[EUR][1000 genomes]
rs61792464	1.00[ASN][1000 genomes]
rs61792535	0.87[EUR][1000 genomes]
rs6446724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828615	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6828882	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834455	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835567	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839081	0.93[EUR][1000 genomes]
rs6839274	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843895	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7438553	0.96[EUR][1000 genomes]
rs7654034	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7663133	1.00[ASN][1000 genomes]
rs7665816	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667354	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682324	1.00[ASN][1000 genomes]
rs7683309	1.00[EUR][1000 genomes]
rs7688390	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993781	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3150000-3174400	Weak transcription	HMEC	breast
4	chr4:3156800-3174000	Weak transcription	A549	lung
5	chr4:3162400-3174000	Weak transcription	Brain Substantia Nigra	brain
6	chr4:3162400-3174000	Weak transcription	Ovary	ovary
7	chr4:3162400-3174200	Weak transcription	NHLF	lung
8	chr4:3162400-3174600	Weak transcription	HUVEC	blood vessel
9	chr4:3162400-3175000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:3162600-3174000	Weak transcription	Colonic Mucosa	Colon
11	chr4:3162600-3174000	Weak transcription	Hela-S3	cervix
12	chr4:3162600-3174000	Weak transcription	HSMM	muscle
13	chr4:3162600-3182200	Weak transcription	Small Intestine	intestine
14	chr4:3162800-3174000	Weak transcription	Aorta	Aorta
15	chr4:3163000-3174000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:3163000-3182000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:3163400-3174200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:3164200-3174400	Weak transcription	Fetal Brain Male	brain
19	chr4:3164600-3174800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:3164800-3174000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:3164800-3174200	Weak transcription	Psoas Muscle	Psoas
22	chr4:3166200-3177400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr4:3168000-3180800	Strong transcription	Fetal Stomach	stomach
25	chr4:3168000-3182600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:3168000-3191800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr4:3168000-3192600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:3168000-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr4:3168600-3174000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:3168600-3174200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:3168800-3174000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:3168800-3174000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:3168800-3174000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr4:3168800-3174000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:3168800-3174000	Weak transcription	Spleen	Spleen
38	chr4:3168800-3174200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:3169000-3174000	Weak transcription	Gastric	stomach
40	chr4:3169200-3174000	Weak transcription	Lung	lung
41	chr4:3169200-3174000	Weak transcription	Thymus	Thymus
42	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
43	chr4:3170200-3174000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:3170200-3174000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:3170200-3174000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:3170200-3174000	Weak transcription	Left Ventricle	heart
47	chr4:3170200-3174000	Weak transcription	Right Ventricle	heart
48	chr4:3170200-3174000	Weak transcription	HSMMtube	muscle
49	chr4:3170200-3174000	Weak transcription	NHDF-Ad	bronchial
50	chr4:3170200-3174200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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