Variant report

Variant	rs3778553
Chromosome Location	chr6:1915364-1915365
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13218267	0.93[YRI][hapmap]
rs1980713	0.90[YRI][hapmap]
rs2875711	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3778552	0.90[EUR][1000 genomes]
rs3800116	0.81[CEU][hapmap];0.93[YRI][hapmap]
rs3800117	0.89[YRI][hapmap]
rs3800119	0.82[YRI][hapmap]
rs4959159	0.83[YRI][hapmap]
rs4959617	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
8	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv883385	chr6:1869592-1915828	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1896000-1916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:1897200-1916200	Weak transcription	Thymus	Thymus
3	chr6:1901600-1923400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:1905000-1970600	Weak transcription	Spleen	Spleen
5	chr6:1905200-1917400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:1905200-1926000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:1905200-1926000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:1905400-1962000	Weak transcription	Pancreas	Pancrea
9	chr6:1908000-1919800	Weak transcription	GM12878-XiMat	blood
10	chr6:1908400-1933600	Weak transcription	Liver	Liver
11	chr6:1909800-1926000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:1910000-1918000	Weak transcription	Lung	lung
13	chr6:1910200-1965800	Weak transcription	Small Intestine	intestine
14	chr6:1911000-1916200	Weak transcription	HMEC	breast
15	chr6:1911200-1916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:1911400-1916000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:1911400-1916200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:1911400-1916400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:1911600-1915400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:1911600-1916200	Weak transcription	HSMMtube	muscle
21	chr6:1911600-1916400	Weak transcription	NHEK	skin
22	chr6:1911600-1916800	Weak transcription	NH-A	brain
23	chr6:1911600-1917000	Weak transcription	NHLF	lung
24	chr6:1911600-1917200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:1911800-1916200	Weak transcription	NHDF-Ad	bronchial
26	chr6:1911800-1917000	Weak transcription	HUVEC	blood vessel
27	chr6:1912000-1916600	Weak transcription	HSMM	muscle
28	chr6:1912200-1916200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:1912200-1916200	Weak transcription	Osteobl	bone
30	chr6:1912200-1916400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:1912400-1916800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:1913000-1916600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:1913000-1918600	Enhancers	Dnd41	blood
34	chr6:1913200-1917200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr6:1914400-1916200	Weak transcription	Brain Anterior Caudate	brain
36	chr6:1914600-1915800	Weak transcription	Right Ventricle	heart
37	chr6:1914800-1915800	Strong transcription	Colonic Mucosa	Colon
38	chr6:1914800-1916000	Strong transcription	Gastric	stomach
39	chr6:1914800-1916000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr6:1914800-1916400	Enhancers	Ovary	ovary
41	chr6:1914800-1916600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:1914800-1916600	Strong transcription	Fetal Intestine Small	intestine
43	chr6:1914800-1930800	Strong transcription	HepG2	liver
44	chr6:1915000-1915600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:1915000-1915800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:1915000-1916200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:1915000-1916600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:1915000-1918200	Strong transcription	Duodenum Mucosa	Duodenum
49	chr6:1915200-1915800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:1915200-1915800	Strong transcription	Fetal Stomach	stomach

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