Variant report

Variant	rs514603
Chromosome Location	chr9:116411259-116411260
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	REST	chr9:116411217-116411725	SK-N-SH	brain:	n/a	chr9:116411407-116411420 chr9:116411570-116411583
2	EP300	chr9:116411169-116411839	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr9:116411240-116411390	HBMEC	blood vessel:	n/a	n/a
4	EP300	chr9:116411075-116411983	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr9:116411240-116411390	SK-N-SH_RA	brain:	n/a	n/a
6	RAD21	chr9:116411212-116411827	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr9:116411240-116411390	AG09319	gingival:	n/a	n/a
8	POLR2A	chr9:116411204-116411836	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr9:116411220-116411370	AG04449	skin:	n/a	n/a
10	NFIC	chr9:116411097-116412056	SK-N-SH	brain:	n/a	chr9:116411589-116411606
11	TCF12	chr9:116410997-116412101	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr9:116411190-116411962	SK-N-SH	brain:	n/a	n/a
13	EP300	chr9:116411222-116411806	SK-N-SH_RA	brain:	n/a	n/a
14	MAX	chr9:116411205-116412004	SK-N-SH	brain:	n/a	chr9:116411424-116411433 chr9:116411423-116411433 chr9:116411425-116411432
15	NFIC	chr9:116411158-116411917	SK-N-SH	brain:	n/a	chr9:116411589-116411606
16	GATA2	chr9:116411248-116411928	SH-SY5Y	brain:	n/a	n/a
17	TCF12	chr9:116411032-116412052	SK-N-SH	brain:	n/a	n/a
18	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	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12005477	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12115627	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12115685	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12115728	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12115730	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12553649	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59042246	0.84[EUR][1000 genomes]
rs680359	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[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:52 , 50 per page) page: 1 2

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	chr9:116409000-116412400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:116409400-116412400	Enhancers	HepG2	liver
7	chr9:116410200-116412000	Enhancers	Right Atrium	heart
8	chr9:116410200-116412600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:116410200-116412800	Enhancers	Placenta	Placenta
10	chr9:116410200-116413400	Enhancers	Fetal Heart	heart
11	chr9:116410200-116413400	Enhancers	NHDF-Ad	bronchial
12	chr9:116410400-116411400	Enhancers	Adipose Nuclei	Adipose
13	chr9:116410400-116411600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr9:116410400-116411800	Enhancers	Rectal Smooth Muscle	rectum
15	chr9:116410400-116412000	Enhancers	Left Ventricle	heart
16	chr9:116410400-116412000	Enhancers	Right Ventricle	heart
17	chr9:116410400-116412000	Enhancers	Stomach Smooth Muscle	stomach
18	chr9:116410400-116412200	Enhancers	Brain Angular Gyrus	brain
19	chr9:116410400-116412200	Enhancers	Brain Anterior Caudate	brain
20	chr9:116410400-116412200	Enhancers	Brain Hippocampus Middle	brain
21	chr9:116410400-116412200	Enhancers	Brain Substantia Nigra	brain
22	chr9:116410400-116412200	Enhancers	Spleen	Spleen
23	chr9:116410400-116412400	Enhancers	Brain Cingulate Gyrus	brain
24	chr9:116410400-116412800	Enhancers	Colon Smooth Muscle	Colon
25	chr9:116410400-116413600	Enhancers	Fetal Muscle Leg	muscle
26	chr9:116410400-116413800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr9:116410400-116415600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:116410600-116411800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr9:116410600-116412000	Enhancers	Brain Germinal Matrix	brain
30	chr9:116410600-116412000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr9:116410600-116412400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:116410600-116413400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:116410600-116413400	Enhancers	NHLF	lung
34	chr9:116410600-116413800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:116410800-116412000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:116410800-116412000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:116410800-116414800	Weak transcription	Fetal Intestine Large	intestine
38	chr9:116411000-116412000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr9:116411000-116412000	Enhancers	Fetal Lung	lung
40	chr9:116411000-116413600	Enhancers	Fetal Stomach	stomach
41	chr9:116411000-116415000	Weak transcription	Fetal Intestine Small	intestine
42	chr9:116411000-116416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:116411200-116411400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:116411200-116411400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:116411200-116411400	Enhancers	Fetal Brain Female	brain
46	chr9:116411200-116411600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:116411200-116411800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr9:116411200-116411800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr9:116411200-116411800	Enhancers	Fetal Brain Male	brain
50	chr9:116411200-116413400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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