Variant report

Variant	rs12554454
Chromosome Location	chr9:97679735-97679736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr9:97679005-97679804	ECC-1	luminal epithelium:	n/a	n/a
2	GATA3	chr9:97679029-97680670	MCF-7	breast:	n/a	chr9:97680287-97680296
3	MAX	chr9:97679158-97680064	MCF-7	breast:	n/a	chr9:97679470-97679479
4	TCF12	chr9:97679139-97679800	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr9:97679048-97679810	ECC-1	luminal epithelium:	n/a	chr9:97679470-97679479
6	TCF12	chr9:97679039-97679791	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr9:97679158-97679848	ECC-1	luminal epithelium:	n/a	chr9:97679470-97679479

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
2	chr9:97572097..97590438-chr9:97672990..97690806,63	MCF-7	breast:
3	chr9:97678393..97680086-chr9:97790321..97791837,2	MCF-7	breast:
4	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
5	chr9:97640729..97643418-chr9:97677399..97680018,2	MCF-7	breast:
6	chr9:97678927..97686235-chr9:97889117..97896057,11	MCF-7	breast:
7	chr9:97678102..97679787-chr9:97854510..97856439,2	MCF-7	breast:
8	chr9:97558473..97564935-chr9:97678907..97687123,11	MCF-7	breast:
9	chr9:97626847..97629665-chr9:97678256..97681885,4	MCF-7	breast:
10	chr9:97623064..97624628-chr9:97679267..97681132,2	MCF-7	breast:
11	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
12	chr9:97654777..97656689-chr9:97679645..97682219,2	MCF-7	breast:
13	chr9:97630097..97631954-chr9:97679073..97680785,2	MCF-7	breast:
14	chr9:97646214..97649715-chr9:97676410..97681725,5	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000230815	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000252153	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10761363	0.84[ASN][1000 genomes]
rs12552838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12553869	1.00[CEU][hapmap]
rs12555128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12555829	1.00[CEU][hapmap]
rs1382411	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382412	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs16911856	1.00[CHB][hapmap]
rs16911862	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2306207	1.00[CEU][hapmap]
rs35322834	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs356133	1.00[AFR][1000 genomes]
rs356145	1.00[AFR][1000 genomes]
rs356147	1.00[AFR][1000 genomes]
rs3910730	0.84[ASN][1000 genomes]
rs41316526	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs456276	1.00[AFR][1000 genomes]
rs4743972	0.84[ASN][1000 genomes]
rs4743973	0.84[ASN][1000 genomes]
rs555799	1.00[AFR][1000 genomes]
rs56198429	1.00[AFR][1000 genomes]
rs56317174	1.00[AFR][1000 genomes]
rs6479582	0.84[ASN][1000 genomes]
rs6479583	0.84[ASN][1000 genomes]
rs66642068	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66863985	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67756624	0.87[AMR][1000 genomes]
rs7022963	0.84[AMR][1000 genomes]
rs7025100	0.84[ASN][1000 genomes]
rs7046900	0.82[EUR][1000 genomes]
rs72747019	1.00[AFR][1000 genomes]
rs72748596	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72748601	0.95[EUR][1000 genomes]
rs72750335	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72750346	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73538177	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867856	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97662600-97680400	Enhancers	Brain Hippocampus Middle	brain
4	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:97670800-97680600	Weak transcription	Ovary	ovary
6	chr9:97671000-97684200	Weak transcription	Small Intestine	intestine
7	chr9:97671600-97681600	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:97672600-97680600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr9:97673000-97681600	Weak transcription	Spleen	Spleen
10	chr9:97674200-97681600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:97674200-97681600	Enhancers	Placenta	Placenta
12	chr9:97675000-97684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:97675200-97681600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:97675400-97681000	Enhancers	Hela-S3	cervix
15	chr9:97675400-97684000	Weak transcription	Psoas Muscle	Psoas
16	chr9:97676600-97683000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:97676600-97684200	Weak transcription	Colonic Mucosa	Colon
18	chr9:97676800-97683400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:97677000-97684000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:97677200-97679800	Weak transcription	Fetal Brain Male	brain
21	chr9:97677200-97680400	Weak transcription	Right Ventricle	heart
22	chr9:97677200-97680600	Weak transcription	Aorta	Aorta
23	chr9:97677200-97680800	Weak transcription	Right Atrium	heart
24	chr9:97677200-97681400	Weak transcription	NHDF-Ad	bronchial
25	chr9:97677200-97681600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:97677200-97681600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr9:97677200-97682000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:97677200-97682000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:97677200-97682600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:97677200-97682600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:97677400-97681400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:97677400-97681600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:97677400-97681600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:97677400-97681600	Weak transcription	NH-A	brain
35	chr9:97677400-97681600	Enhancers	NHEK	skin
36	chr9:97677400-97681600	Weak transcription	Osteobl	bone
37	chr9:97677400-97688600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:97678000-97680400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:97678000-97681400	Weak transcription	HSMMtube	muscle
40	chr9:97678000-97681600	Weak transcription	NHLF	lung
41	chr9:97678000-97682600	Weak transcription	Brain Germinal Matrix	brain
42	chr9:97678000-97683000	Weak transcription	Fetal Intestine Large	intestine
43	chr9:97678000-97684400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:97678200-97681600	Weak transcription	Fetal Stomach	stomach
45	chr9:97678200-97681600	Weak transcription	Left Ventricle	heart
46	chr9:97678200-97681600	Weak transcription	HSMM	muscle
47	chr9:97678200-97682600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr9:97679000-97679800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr9:97679000-97679800	Enhancers	Muscle Satellite Cultured Cells	--
50	chr9:97679000-97680000	Enhancers	HUES64 Cell Line	embryonic stem cell

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