Variant report

Variant	rs9446988
Chromosome Location	chr6:74415076-74415077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74404829..74407849-chr6:74412621..74415207,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231652	Chromatin interaction
ENSG00000156535	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs55982851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56171536	0.83[EUR][1000 genomes]
rs56311419	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72953369	0.94[EUR][1000 genomes]
rs72953372	0.86[EUR][1000 genomes]
rs72953375	0.94[EUR][1000 genomes]
rs9442946	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9442947	1.00[ASW][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9446984	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446986	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
6	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv463154	chr6:74412048-74775904	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv603695	chr6:74412048-74775904	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr6:74407200-74421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:74407200-74422400	Weak transcription	Fetal Lung	lung
3	chr6:74407200-74423800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:74407200-74424800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:74407400-74423000	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:74407600-74424000	Weak transcription	Right Ventricle	heart
7	chr6:74407800-74415800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:74407800-74416800	Weak transcription	Thymus	Thymus
9	chr6:74408000-74446800	Weak transcription	Dnd41	blood
10	chr6:74410000-74415800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:74410800-74417400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:74411600-74415400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:74411800-74415800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:74412400-74415400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:74412400-74417400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:74412800-74415400	Enhancers	NHLF	lung
17	chr6:74412800-74423600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:74413000-74415200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr6:74413000-74415200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:74413000-74415400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr6:74413000-74416200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:74413400-74415200	Enhancers	Colon Smooth Muscle	Colon
23	chr6:74413400-74415200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:74413600-74415400	Enhancers	Rectal Smooth Muscle	rectum
25	chr6:74413600-74422200	Weak transcription	Fetal Heart	heart
26	chr6:74414000-74415200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:74414200-74416600	Weak transcription	Lung	lung
28	chr6:74414400-74415200	Enhancers	Adipose Nuclei	Adipose
29	chr6:74414400-74423000	Weak transcription	Primary T cells from cord blood	blood
30	chr6:74414400-74423200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:74414400-74424000	Weak transcription	Placenta	Placenta
32	chr6:74414600-74420400	Weak transcription	Brain Anterior Caudate	brain
33	chr6:74414600-74423000	Weak transcription	Fetal Thymus	thymus
34	chr6:74414800-74415200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr6:74414800-74415200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:74414800-74415600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:74414800-74415600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:74414800-74415800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:74414800-74416200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:74414800-74416200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:74414800-74416200	Genic enhancers	NHDF-Ad	bronchial
42	chr6:74414800-74416600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:74414800-74417000	Genic enhancers	HMEC	breast
44	chr6:74414800-74417600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:74414800-74420400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:74414800-74420400	Weak transcription	Left Ventricle	heart
47	chr6:74414800-74422600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:74414800-74423200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr6:74414800-74474600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:74415000-74415200	Genic enhancers	NHEK	skin

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