Variant report

Variant	rs3778561
Chromosome Location	chr6:2162644-2162645
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:2161158..2164138-chr9:131314660..131316336,2	MCF-7	breast:
2	chr6:2162382..2163882-chr7:156518679..156520785,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228395	Chromatin interaction
ENSG00000197694	Chromatin interaction
ENSG00000105983	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs108035	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1332792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs163073	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs234944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs234951	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3800159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4959168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6596873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	nsv522608	chr6:2032259-2203888	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv883387	chr6:2086679-2176239	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
11	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
12	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2157600-2164400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:2158200-2164400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:2159200-2163000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:2159200-2163600	Weak transcription	Gastric	stomach
5	chr6:2159200-2166800	Weak transcription	A549	lung
6	chr6:2161000-2163400	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:2161000-2163800	Enhancers	Hela-S3	cervix
8	chr6:2161600-2162800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:2161600-2163000	Enhancers	NHLF	lung
10	chr6:2161600-2163400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr6:2161600-2163400	Enhancers	HepG2	liver
12	chr6:2161600-2163600	Enhancers	HMEC	breast
13	chr6:2161600-2163600	Enhancers	Osteobl	bone
14	chr6:2161600-2163800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:2161600-2163800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:2161600-2163800	Enhancers	Dnd41	blood
17	chr6:2161800-2162800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:2161800-2162800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:2161800-2163000	Enhancers	NH-A	brain
20	chr6:2161800-2163200	Enhancers	Primary T cells from cord blood	blood
21	chr6:2161800-2163200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:2161800-2163200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:2161800-2163200	Enhancers	Left Ventricle	heart
24	chr6:2161800-2163200	Enhancers	HSMM	muscle
25	chr6:2161800-2163400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:2161800-2163400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:2161800-2163400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:2161800-2163400	Enhancers	HSMMtube	muscle
29	chr6:2161800-2163400	Enhancers	HUVEC	blood vessel
30	chr6:2161800-2163600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:2161800-2163600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:2161800-2163600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:2161800-2163600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:2161800-2163600	Enhancers	Primary B cells from peripheral blood	blood
35	chr6:2161800-2163600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr6:2161800-2163800	Enhancers	Pancreas	Pancrea
37	chr6:2161800-2163800	Enhancers	Small Intestine	intestine
38	chr6:2162000-2162800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:2162000-2162800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr6:2162000-2163200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:2162000-2163200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:2162000-2163200	Enhancers	Adipose Nuclei	Adipose
43	chr6:2162000-2163200	Enhancers	NHEK	skin
44	chr6:2162000-2163600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:2162000-2163800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:2162200-2162800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:2162200-2162800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr6:2162200-2163600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:2162200-2163600	Enhancers	GM12878-XiMat	blood
50	chr6:2162400-2163200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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