Variant report

Variant	rs3799850
Chromosome Location	chr6:110051882-110051883
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:110047914..110050234-chr6:110051143..110053248,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1321329	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1535419	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1535420	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17070657	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17070666	0.86[EUR][1000 genomes]
rs17070692	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17070701	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17070705	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs17070733	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070737	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070740	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070743	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070803	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17070833	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17070875	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17070915	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17070921	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17070937	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799844	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799848	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4454171	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57181024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57996937	0.86[EUR][1000 genomes]
rs58273806	0.86[EUR][1000 genomes]
rs58731181	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59203807	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59626863	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60108304	0.86[EUR][1000 genomes]
rs60927725	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61374793	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61522207	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61671496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9487143	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9791294	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
2	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
3	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
5	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:110024200-110056400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:110025000-110057000	Weak transcription	Fetal Thymus	thymus
9	chr6:110027000-110052400	Weak transcription	Liver	Liver
10	chr6:110027000-110056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr6:110028200-110057200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:110034400-110060800	Weak transcription	Fetal Stomach	stomach
15	chr6:110034600-110056400	Weak transcription	Fetal Brain Female	brain
16	chr6:110034600-110057000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr6:110034800-110059000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
20	chr6:110035200-110056200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:110035200-110065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:110035400-110057800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
25	chr6:110035600-110056400	Weak transcription	Ovary	ovary
26	chr6:110035600-110057000	Weak transcription	Pancreas	Pancrea
27	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
28	chr6:110035800-110057000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:110035800-110065000	Weak transcription	HSMM	muscle
30	chr6:110036200-110056200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:110036600-110057000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
33	chr6:110037200-110056000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:110037200-110056000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:110037600-110057000	Weak transcription	Psoas Muscle	Psoas
36	chr6:110038000-110056400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:110038000-110057000	Weak transcription	Fetal Intestine Large	intestine
38	chr6:110038400-110056400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:110039000-110054600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:110039000-110056400	Weak transcription	Placenta	Placenta
41	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr6:110039200-110057000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:110039200-110058800	Weak transcription	Colon Smooth Muscle	Colon
44	chr6:110039600-110053400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:110039600-110056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:110039600-110057000	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:110039800-110062000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:110040400-110056400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr6:110040800-110062000	Weak transcription	Thymus	Thymus
50	chr6:110041000-110056000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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