Variant report

Variant	rs4744180
Chromosome Location	chr9:95906804-95906805
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	RFX5	chr9:95906013-95906952	SK-N-SH	brain:	n/a	chr9:95906531-95906546 chr9:95906535-95906544
2	MAX	chr9:95906108-95906870	ECC-1	luminal epithelium:	n/a	chr9:95906556-95906563 chr9:95906555-95906564 chr9:95906554-95906564
3	NFIC	chr9:95906110-95906837	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr9:95906518-95906938	ECC-1	luminal epithelium:	n/a	n/a
5	NR3C1	chr9:95906621-95906871	A549	lung:	n/a	n/a
6	NR3C1	chr9:95906526-95906914	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95895264..95898192-chr9:95905640..95908548,4	MCF-7	breast:
2	chr9:95905509..95907695-chr9:96212278..96215177,2	MCF-7	breast:
3	chr9:95890205..95893165-chr9:95905253..95907697,2	MCF-7	breast:
4	chr9:95902234..95904714-chr9:95904881..95906837,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203364	TF binding region
ENSG00000188938	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10114849	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10739943	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10761196	0.95[ASN][1000 genomes]
rs10992649	1.00[AFR][1000 genomes]
rs10992654	1.00[AFR][1000 genomes]
rs10992656	1.00[AFR][1000 genomes]
rs1419232	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1936400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2398826	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743893	0.96[ASN][1000 genomes]
rs4743895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479455	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6479456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7847349	0.95[ASN][1000 genomes]
rs7867718	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95899600-95907200	Enhancers	Fetal Thymus	thymus
2	chr9:95899800-95907400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr9:95899800-95922200	Weak transcription	Gastric	stomach
4	chr9:95901600-95907800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr9:95901800-95907400	Enhancers	Primary T cells from cord blood	blood
6	chr9:95902400-95907400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:95903000-95907600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:95904000-95907200	Enhancers	Fetal Muscle Leg	muscle
9	chr9:95904200-95907000	Enhancers	Fetal Muscle Trunk	muscle
10	chr9:95904200-95907200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr9:95904200-95907200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:95904400-95907200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:95904800-95911600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:95905000-95907000	Enhancers	Primary B cells from peripheral blood	blood
15	chr9:95905200-95907800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:95905400-95907000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:95905400-95907200	Enhancers	Pancreas	Pancrea
18	chr9:95905600-95907000	Enhancers	Colonic Mucosa	Colon
19	chr9:95905600-95907200	Enhancers	HMEC	breast
20	chr9:95905600-95907400	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:95905600-95907400	Enhancers	Dnd41	blood
22	chr9:95905600-95907600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:95906000-95907000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr9:95906000-95907000	Enhancers	Lung	lung
25	chr9:95906000-95907000	Enhancers	GM12878-XiMat	blood
26	chr9:95906200-95907000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr9:95906200-95907000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr9:95906200-95907000	Enhancers	Primary B cells from cord blood	blood
29	chr9:95906200-95907000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr9:95906200-95907000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr9:95906200-95907000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:95906200-95907000	Enhancers	Adipose Nuclei	Adipose
33	chr9:95906200-95907000	Enhancers	Aorta	Aorta
34	chr9:95906200-95907000	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr9:95906200-95907000	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr9:95906200-95907000	Enhancers	Colon Smooth Muscle	Colon
37	chr9:95906200-95907000	Enhancers	Fetal Stomach	stomach
38	chr9:95906200-95907000	Enhancers	Left Ventricle	heart
39	chr9:95906200-95907000	Enhancers	Rectal Smooth Muscle	rectum
40	chr9:95906200-95907000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr9:95906200-95907000	Enhancers	Thymus	Thymus
42	chr9:95906200-95907000	Enhancers	Spleen	Spleen
43	chr9:95906200-95907000	Enhancers	A549	lung
44	chr9:95906200-95907000	Enhancers	HSMMtube	muscle
45	chr9:95906200-95907000	Enhancers	HUVEC	blood vessel
46	chr9:95906200-95907000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr9:95906200-95907200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:95906200-95907200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr9:95906200-95907200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:95906200-95907200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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