Variant report

Variant	rs9491980
Chromosome Location	chr6:128838904-128838905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:128582093..128584697-chr6:128837885..128840735,2	MCF-7	breast:
2	chr6:128401254..128402898-chr6:128838085..128840058,2	MCF-7	breast:
3	chr6:128810906..128814817-chr6:128838628..128842024,3	MCF-7	breast:
4	chr6:128838418..128841487-chr6:128915011..128917718,3	MCF-7	breast:
5	chr6:128412558..128415332-chr6:128836594..128839450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1341601	0.92[AFR][1000 genomes]
rs766305	0.92[AFR][1000 genomes]
rs7749797	0.85[YRI][hapmap]
rs9321123	0.86[AFR][1000 genomes]
rs9482896	0.92[AFR][1000 genomes]
rs9482899	0.80[AFR][1000 genomes]
rs9491978	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9491979	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9491981	0.92[AFR][1000 genomes]
rs9491982	0.92[AFR][1000 genomes]
rs9491987	0.92[AFR][1000 genomes]
rs9491989	0.92[AFR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS 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	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
3	chr6:128825800-128840000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:128829400-128839400	Weak transcription	Colonic Mucosa	Colon
5	chr6:128829400-128839600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:128830000-128839600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:128831400-128840000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:128831600-128839800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:128832200-128839400	Enhancers	Liver	Liver
10	chr6:128832600-128839600	Weak transcription	Gastric	stomach
11	chr6:128832800-128839600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:128832800-128839800	Weak transcription	Right Ventricle	heart
13	chr6:128834200-128839000	Enhancers	A549	lung
14	chr6:128834800-128839000	Enhancers	Stomach Mucosa	stomach
15	chr6:128835000-128840600	Active TSS	Fetal Brain Female	brain
16	chr6:128835200-128839200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:128835800-128839600	Enhancers	Fetal Lung	lung
18	chr6:128835800-128839800	Weak transcription	Small Intestine	intestine
19	chr6:128836400-128839600	Enhancers	Rectal Smooth Muscle	rectum
20	chr6:128836600-128839200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:128836600-128839400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:128836800-128839400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:128837000-128840000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:128837200-128839000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:128837200-128839000	Flanking Active TSS	NH-A	brain
26	chr6:128837200-128839800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:128837200-128842800	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr6:128837400-128839000	Flanking Active TSS	HepG2	liver
29	chr6:128837400-128839000	Flanking Active TSS	NHEK	skin
30	chr6:128837400-128839600	Weak transcription	Placenta	Placenta
31	chr6:128837400-128839600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:128837600-128839600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:128837600-128839600	Enhancers	Fetal Kidney	kidney
34	chr6:128837600-128839800	Weak transcription	Psoas Muscle	Psoas
35	chr6:128837600-128840000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr6:128837800-128839000	Enhancers	Brain Substantia Nigra	brain
37	chr6:128837800-128839200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:128837800-128839400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:128837800-128839600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:128837800-128839600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:128838000-128839200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:128838000-128839600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:128838000-128839600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:128838000-128839600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:128838000-128839800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:128838200-128839200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:128838200-128839400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:128838200-128839400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:128838200-128839600	Flanking Active TSS	NHLF	lung
50	chr6:128838200-128842400	Active TSS	Brain Cingulate Gyrus	brain

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