Variant report

Variant	rs4979178
Chromosome Location	chr9:115644335-115644336
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115634993..115639011-chr9:115640065..115646725,6	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10114602	0.95[EUR][1000 genomes]
rs10114623	0.95[EUR][1000 genomes]
rs10115576	0.85[CEU][hapmap]
rs10116897	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1041086	0.86[EUR][1000 genomes]
rs10733598	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10733599	0.85[CEU][hapmap]
rs10739376	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10739377	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10739378	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs10739379	0.92[EUR][1000 genomes]
rs10759590	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10759603	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs10759604	0.92[EUR][1000 genomes]
rs10817402	0.81[JPT][hapmap]
rs10981534	0.95[EUR][1000 genomes]
rs1324930	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1324931	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs1324932	0.86[CEU][hapmap];0.95[EUR][1000 genomes]
rs1475293	0.85[CEU][hapmap]
rs2025544	0.85[CEU][hapmap]
rs41301513	0.85[ASN][1000 genomes]
rs4978509	0.95[EUR][1000 genomes]
rs4979170	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs4979173	0.86[EUR][1000 genomes]
rs4979175	0.95[EUR][1000 genomes]
rs4979176	0.92[EUR][1000 genomes]
rs4979177	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62576453	0.93[EUR][1000 genomes]
rs7023956	0.88[EUR][1000 genomes]
rs7047914	0.85[EUR][1000 genomes]
rs7873289	0.85[CEU][hapmap];0.92[EUR][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	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115615600-115646400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:115624200-115652600	Weak transcription	Fetal Heart	heart
3	chr9:115625800-115645200	Weak transcription	Thymus	Thymus
4	chr9:115626400-115650800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:115627000-115647000	Weak transcription	Colonic Mucosa	Colon
6	chr9:115627600-115646800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:115630600-115646400	Weak transcription	Fetal Lung	lung
8	chr9:115630600-115647200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:115630800-115646400	Weak transcription	Placenta	Placenta
10	chr9:115631200-115646400	Weak transcription	Fetal Kidney	kidney
11	chr9:115631800-115646400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:115631800-115652200	Weak transcription	Gastric	stomach
13	chr9:115632200-115644800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:115633000-115645800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr9:115633000-115646400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:115633000-115652600	Weak transcription	Left Ventricle	heart
17	chr9:115633200-115646400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:115633200-115652400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:115633200-115652400	Weak transcription	Right Ventricle	heart
20	chr9:115633400-115646800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:115633400-115648200	Weak transcription	Esophagus	oesophagus
22	chr9:115633400-115649200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr9:115633600-115644400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr9:115633800-115652600	Weak transcription	Liver	Liver
25	chr9:115634600-115646400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr9:115634800-115646400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr9:115634800-115651800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:115635000-115650800	Weak transcription	Fetal Thymus	thymus
29	chr9:115635600-115649000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr9:115636000-115648600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr9:115636600-115646400	Weak transcription	NHDF-Ad	bronchial
32	chr9:115638200-115647000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:115638600-115650000	Weak transcription	Fetal Brain Female	brain
34	chr9:115640400-115644800	Weak transcription	Psoas Muscle	Psoas
35	chr9:115640800-115647000	Weak transcription	Primary T cells from cord blood	blood
36	chr9:115641000-115646400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:115642200-115644800	Strong transcription	Fetal Stomach	stomach
38	chr9:115643000-115645600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr9:115643200-115644400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:115643200-115644400	Enhancers	HSMMtube	muscle
41	chr9:115643200-115652600	Weak transcription	Brain Anterior Caudate	brain
42	chr9:115643200-115652800	Weak transcription	Ovary	ovary
43	chr9:115643400-115644400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr9:115643400-115644400	Enhancers	HMEC	breast
45	chr9:115643400-115645400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:115643400-115646400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:115643400-115651600	Weak transcription	Primary B cells from cord blood	blood
48	chr9:115643400-115652400	Weak transcription	Brain Substantia Nigra	brain
49	chr9:115643600-115644400	Enhancers	HSMM	muscle
50	chr9:115643600-115646400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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