Variant report

Variant	rs6782429
Chromosome Location	chr3:45936559-45936560
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	chr3:45928724..45930897-chr3:45935316..45937511,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CXCR6-1	chr3:45936398-45936600	NONHSAT089421

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1078355	1.00[EUR][1000 genomes]
rs35423527	1.00[AMR][1000 genomes]
rs56817174	1.00[EUR][1000 genomes]
rs59028610	1.00[EUR][1000 genomes]
rs60760320	1.00[EUR][1000 genomes]
rs6782398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6783694	1.00[EUR][1000 genomes]
rs6800925	1.00[EUR][1000 genomes]
rs72876559	1.00[AMR][1000 genomes]
rs72876563	1.00[AMR][1000 genomes]
rs72876570	1.00[AMR][1000 genomes]
rs72883072	1.00[AMR][1000 genomes]
rs72883074	1.00[AMR][1000 genomes]
rs72883076	1.00[AMR][1000 genomes]
rs72883078	1.00[AMR][1000 genomes]
rs72883080	1.00[AMR][1000 genomes]
rs72884909	1.00[AMR][1000 genomes]
rs72884914	1.00[AMR][1000 genomes]
rs72884918	1.00[AMR][1000 genomes]
rs72885402	1.00[EUR][1000 genomes]
rs72887108	1.00[EUR][1000 genomes]
rs72890672	1.00[AMR][1000 genomes]
rs72890685	1.00[EUR][1000 genomes]
rs72890688	1.00[EUR][1000 genomes]
rs72890691	1.00[EUR][1000 genomes]
rs72890697	1.00[EUR][1000 genomes]
rs7653195	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45923400-45948200	Weak transcription	Right Atrium	heart
2	chr3:45925200-45949600	Weak transcription	Pancreas	Pancrea
3	chr3:45925600-45947800	Genic enhancers	Dnd41	blood
4	chr3:45928800-45936600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
5	chr3:45929800-45936600	Enhancers	Primary B cells from cord blood	blood
6	chr3:45929800-45936600	Enhancers	Primary B cells from peripheral blood	blood
7	chr3:45932400-45936600	Weak transcription	Fetal Stomach	stomach
8	chr3:45932400-45960200	Weak transcription	Fetal Intestine Small	intestine
9	chr3:45933600-45937800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:45934000-45936800	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:45934000-45960200	Weak transcription	Right Ventricle	heart
12	chr3:45934200-45936600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:45934200-45938400	Weak transcription	Aorta	Aorta
14	chr3:45934600-45936800	Enhancers	Primary T cells from cord blood	blood
15	chr3:45934600-45946200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:45935000-45936600	Transcr. at gene 5' and 3'	Thymus	Thymus
17	chr3:45935400-45936600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:45935400-45941200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:45935400-45945000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:45936000-45936600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:45936000-45936800	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:45936000-45937600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:45936000-45937600	Weak transcription	Placenta	Placenta
24	chr3:45936000-45947600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:45936200-45936600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:45936200-45936800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:45936200-45939400	Enhancers	Hela-S3	cervix
28	chr3:45936400-45936600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr3:45936400-45936600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:45936400-45936600	Enhancers	HSMM	muscle
31	chr3:45936400-45936600	Bivalent Enhancer	K562	blood
32	chr3:45936400-45937200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:45936400-45937400	Enhancers	NHEK	skin
34	chr3:45936400-45939200	Enhancers	HMEC	breast

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