Variant report

Variant	rs3799281
Chromosome Location	chr6:73890628-73890629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:73844216..73844877-chr6:73890551..73891344,2	MCF-7	breast:
2	chr6:73121678..73122602-chr6:73890471..73891079,4	MCF-7	breast:
3	chr6:73890367..73891378-chr6:74036227..74036958,3	MCF-7	breast:
4	chr6:73121565..73122677-chr6:73889848..73891063,3	K562	blood:
5	chr6:73326001..73326770-chr6:73890518..73891023,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12660923	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12661161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661261	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12662303	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662357	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12662682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662788	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12662803	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12662818	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12662845	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12664116	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16883459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883483	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16883489	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34320997	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35791353	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3799279	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799287	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3823120	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41265511	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4631235	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56776915	0.92[AFR][1000 genomes]
rs56941368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57781909	0.80[AMR][1000 genomes]
rs57919814	0.81[EUR][1000 genomes]
rs58424716	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58519898	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59789863	0.88[EUR][1000 genomes]
rs59860080	0.92[AFR][1000 genomes]
rs60111089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60710559	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60998603	0.88[EUR][1000 genomes]
rs6919519	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7771861	1.00[CEU][hapmap];1.00[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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73869000-73904200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:73884800-73903600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:73887600-73903600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:73889600-73890800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:73890000-73890800	Enhancers	HMEC	breast
6	chr6:73890000-73891200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr6:73890200-73890800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:73890200-73890800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:73890200-73890800	Enhancers	Psoas Muscle	Psoas
10	chr6:73890200-73890800	Enhancers	Right Atrium	heart
11	chr6:73890200-73891000	Flanking Active TSS	GM12878-XiMat	blood
12	chr6:73890200-73891400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:73890400-73890800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr6:73890400-73890800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:73890400-73890800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:73890400-73890800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr6:73890400-73890800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:73890400-73890800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:73890400-73890800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:73890400-73890800	Active TSS	Aorta	Aorta
21	chr6:73890400-73890800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr6:73890400-73890800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:73890400-73890800	Active TSS	Fetal Lung	lung
24	chr6:73890400-73890800	Enhancers	Fetal Muscle Trunk	muscle
25	chr6:73890400-73890800	Enhancers	Fetal Muscle Leg	muscle
26	chr6:73890400-73890800	Enhancers	Ovary	ovary
27	chr6:73890400-73890800	Active TSS	Rectal Smooth Muscle	rectum
28	chr6:73890400-73890800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr6:73890400-73890800	Flanking Active TSS	NH-A	brain
30	chr6:73890400-73891000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:73890400-73891000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:73890400-73891000	Active TSS	Brain Anterior Caudate	brain
33	chr6:73890400-73891000	Active TSS	Stomach Smooth Muscle	stomach
34	chr6:73890400-73891000	Active TSS	HSMM	muscle
35	chr6:73890400-73891000	Active TSS	HSMMtube	muscle
36	chr6:73890400-73891000	Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:73890400-73891000	Flanking Active TSS	NHEK	skin
38	chr6:73890400-73891000	Active TSS	NHLF	lung
39	chr6:73890400-73891200	Enhancers	Fetal Brain Female	brain
40	chr6:73890600-73890800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:73890600-73890800	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr6:73890600-73890800	Flanking Active TSS	Liver	Liver
43	chr6:73890600-73890800	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr6:73890600-73890800	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr6:73890600-73890800	Enhancers	Fetal Heart	heart
46	chr6:73890600-73890800	Flanking Active TSS	A549	lung
47	chr6:73890600-73891000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:73890600-73891000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:73890600-73891000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:73890600-73891000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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