Variant report

Variant	rs680359
Chromosome Location	chr9:116411591-116411592
allele	A/G
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	POLR2A	chr9:116411305-116411673	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr9:116411271-116411968	SK-N-SH	brain:	n/a	n/a
3	REST	chr9:116411217-116411725	SK-N-SH	brain:	n/a	chr9:116411407-116411420 chr9:116411570-116411583
4	EP300	chr9:116411169-116411839	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr9:116411480-116411630	AG04449	skin:	n/a	chr9:116411547-116411560 chr9:116411544-116411562
6	EP300	chr9:116411075-116411983	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr9:116411277-116411679	SK-N-SH_RA	brain:	n/a	n/a
8	RAD21	chr9:116411212-116411827	SK-N-SH_RA	brain:	n/a	n/a
9	FOXP2	chr9:116411393-116411695	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr9:116411204-116411836	SK-N-SH	brain:	n/a	n/a
11	YY1	chr9:116411300-116411914	SK-N-SH_RA	brain:	n/a	chr9:116411740-116411750 chr9:116411740-116411762
12	SIN3AK20	chr9:116411348-116411722	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr9:116411097-116412056	SK-N-SH	brain:	n/a	chr9:116411589-116411606
14	REST	chr9:116411425-116411727	SK-N-SH	brain:	n/a	chr9:116411570-116411583
15	TCF12	chr9:116410997-116412101	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr9:116411190-116411962	SK-N-SH	brain:	n/a	n/a
17	EP300	chr9:116411222-116411806	SK-N-SH_RA	brain:	n/a	n/a
18	MAX	chr9:116411205-116412004	SK-N-SH	brain:	n/a	chr9:116411424-116411433 chr9:116411423-116411433 chr9:116411425-116411432
19	NFIC	chr9:116411158-116411917	SK-N-SH	brain:	n/a	chr9:116411589-116411606
20	GATA2	chr9:116411248-116411928	SH-SY5Y	brain:	n/a	n/a
21	TCF12	chr9:116411032-116412052	SK-N-SH	brain:	n/a	n/a
22	REST	chr9:116411471-116411766	SK-N-SH	brain:	n/a	chr9:116411570-116411583
23	YY1	chr9:116411426-116411864	SK-N-SH_RA	brain:	n/a	chr9:116411740-116411750 chr9:116411740-116411762
24	MAX	chr9:116411173-116412015	SK-N-SH	brain:	n/a	chr9:116411424-116411433 chr9:116411423-116411433 chr9:116411425-116411432

No.	Distal block	Cell Line	Cell type
1	chr9:116410830..116412902-chr9:116418886..116421304,2	MCF-7	breast:
2	chr9:116396277..116398394-chr9:116409096..116411903,2	MCF-7	breast:
3	chr9:116409796..116412169-chr9:116418517..116420512,2	MCF-7	breast:
4	chr9:116385537..116387562-chr9:116409870..116412944,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227482	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10981864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115627	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115685	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115728	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12115730	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514603	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59042246	0.84[EUR][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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116407000-116413600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:116407800-116412600	Weak transcription	Fetal Kidney	kidney
3	chr9:116408200-116412600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:116409000-116412400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:116409400-116412400	Enhancers	HepG2	liver
6	chr9:116410200-116412000	Enhancers	Right Atrium	heart
7	chr9:116410200-116412600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:116410200-116412800	Enhancers	Placenta	Placenta
9	chr9:116410200-116413400	Enhancers	Fetal Heart	heart
10	chr9:116410200-116413400	Enhancers	NHDF-Ad	bronchial
11	chr9:116410400-116411600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:116410400-116411800	Enhancers	Rectal Smooth Muscle	rectum
13	chr9:116410400-116412000	Enhancers	Left Ventricle	heart
14	chr9:116410400-116412000	Enhancers	Right Ventricle	heart
15	chr9:116410400-116412000	Enhancers	Stomach Smooth Muscle	stomach
16	chr9:116410400-116412200	Enhancers	Brain Angular Gyrus	brain
17	chr9:116410400-116412200	Enhancers	Brain Anterior Caudate	brain
18	chr9:116410400-116412200	Enhancers	Brain Hippocampus Middle	brain
19	chr9:116410400-116412200	Enhancers	Brain Substantia Nigra	brain
20	chr9:116410400-116412200	Enhancers	Spleen	Spleen
21	chr9:116410400-116412400	Enhancers	Brain Cingulate Gyrus	brain
22	chr9:116410400-116412800	Enhancers	Colon Smooth Muscle	Colon
23	chr9:116410400-116413600	Enhancers	Fetal Muscle Leg	muscle
24	chr9:116410400-116413800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr9:116410400-116415600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:116410600-116411800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr9:116410600-116412000	Enhancers	Brain Germinal Matrix	brain
28	chr9:116410600-116412000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr9:116410600-116412400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:116410600-116413400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:116410600-116413400	Enhancers	NHLF	lung
32	chr9:116410600-116413800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:116410800-116412000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:116410800-116412000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:116410800-116414800	Weak transcription	Fetal Intestine Large	intestine
36	chr9:116411000-116412000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:116411000-116412000	Enhancers	Fetal Lung	lung
38	chr9:116411000-116413600	Enhancers	Fetal Stomach	stomach
39	chr9:116411000-116415000	Weak transcription	Fetal Intestine Small	intestine
40	chr9:116411000-116416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:116411200-116411600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:116411200-116411800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr9:116411200-116411800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr9:116411200-116411800	Enhancers	Fetal Brain Male	brain
45	chr9:116411200-116413400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:116411200-116413400	Enhancers	Ovary	ovary
47	chr9:116411200-116415400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:116411400-116412400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:116411400-116413800	Enhancers	HUVEC	blood vessel
50	chr9:116411400-116415400	Enhancers	Osteobl	bone

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