Variant report

Variant	rs4978551
Chromosome Location	chr9:116410660-116410661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr9:116410441-116410761	ECC-1	luminal epithelium:	n/a	chr9:116410581-116410596 chr9:116410517-116410532
2	ESR1	chr9:116410366-116410788	ECC-1	luminal epithelium:	n/a	chr9:116410581-116410596 chr9:116410517-116410532
3	ESR1	chr9:116410294-116410821	ECC-1	luminal epithelium:	n/a	chr9:116410581-116410596 chr9:116410517-116410532

No.	Distal block	Cell Line	Cell type
1	chr9:116408801..116410692-chr9:116411942..116414922,2	MCF-7	breast:
2	chr9:116355237..116358414-chr9:116407297..116411060,4	MCF-7	breast:
3	chr9:116396277..116398394-chr9:116409096..116411903,2	MCF-7	breast:
4	chr9:116409796..116412169-chr9:116418517..116420512,2	MCF-7	breast:
5	chr9:116385537..116387562-chr9:116409870..116412944,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227482	TF binding region
ENSG00000138835	Chromatin interaction
ENSG00000227482	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10817497	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10981859	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10981860	0.84[ASN][1000 genomes]
rs4979270	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers 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 miRNA target site	165 gene(s)	inside rSNPs	diseases
4	nsv893749	chr9:116378759-116439749	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116406400-116411400	Weak transcription	HUVEC	blood vessel
2	chr9:116407000-116413600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:116407800-116412600	Weak transcription	Fetal Kidney	kidney
4	chr9:116408200-116412600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:116408600-116411200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:116409000-116412400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:116409400-116412400	Enhancers	HepG2	liver
8	chr9:116409600-116411200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:116410000-116411000	Enhancers	Fetal Intestine Small	intestine
10	chr9:116410200-116410800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:116410200-116410800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr9:116410200-116410800	Enhancers	Fetal Intestine Large	intestine
13	chr9:116410200-116412000	Enhancers	Right Atrium	heart
14	chr9:116410200-116412600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:116410200-116412800	Enhancers	Placenta	Placenta
16	chr9:116410200-116413400	Enhancers	Fetal Heart	heart
17	chr9:116410200-116413400	Enhancers	NHDF-Ad	bronchial
18	chr9:116410400-116410800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:116410400-116411400	Enhancers	Adipose Nuclei	Adipose
20	chr9:116410400-116411600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr9:116410400-116411800	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:116410400-116412000	Enhancers	Left Ventricle	heart
23	chr9:116410400-116412000	Enhancers	Right Ventricle	heart
24	chr9:116410400-116412000	Enhancers	Stomach Smooth Muscle	stomach
25	chr9:116410400-116412200	Enhancers	Brain Angular Gyrus	brain
26	chr9:116410400-116412200	Enhancers	Brain Anterior Caudate	brain
27	chr9:116410400-116412200	Enhancers	Brain Hippocampus Middle	brain
28	chr9:116410400-116412200	Enhancers	Brain Substantia Nigra	brain
29	chr9:116410400-116412200	Enhancers	Spleen	Spleen
30	chr9:116410400-116412400	Enhancers	Brain Cingulate Gyrus	brain
31	chr9:116410400-116412800	Enhancers	Colon Smooth Muscle	Colon
32	chr9:116410400-116413600	Enhancers	Fetal Muscle Leg	muscle
33	chr9:116410400-116413800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:116410400-116415600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:116410600-116410800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr9:116410600-116411800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr9:116410600-116412000	Enhancers	Brain Germinal Matrix	brain
38	chr9:116410600-116412000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr9:116410600-116412400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:116410600-116413400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:116410600-116413400	Enhancers	NHLF	lung
42	chr9:116410600-116413800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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