Variant report

Variant	rs4977280
Chromosome Location	chr9:19095849-19095850
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	STAT3	chr9:19095743-19095856	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19095545..19097905-chr9:19098403..19100459,2	K562	blood:
2	chr9:19095602..19097894-chr9:19377705..19380132,2	MCF-7	breast:

Variant related genes	Relation type
HAUS6	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10122088	0.93[CEU][hapmap]
rs10757026	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12349207	0.87[CEU][hapmap]
rs2171956	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2291503	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4977488	0.81[EUR][1000 genomes]
rs4977491	0.85[EUR][1000 genomes]
rs6415731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6475303	0.81[CEU][hapmap]
rs7042340	0.95[EUR][1000 genomes]
rs7042382	0.86[CEU][hapmap]
rs7048069	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9298798	1.00[CEU][hapmap];0.94[EUR][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	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv2764156	chr9:19076894-19097008	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv870340	chr9:19077714-19143230	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1018947	chr9:19094894-19394712	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4977280	ADFP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:19056600-19096000	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:19056800-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:19062000-19102200	Weak transcription	Stomach Mucosa	stomach
12	chr9:19066400-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:19066800-19100400	Weak transcription	Fetal Heart	heart
14	chr9:19066800-19100800	Weak transcription	Small Intestine	intestine
15	chr9:19068800-19096800	Strong transcription	Fetal Thymus	thymus
16	chr9:19071200-19101200	Weak transcription	Psoas Muscle	Psoas
17	chr9:19073600-19098400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:19077400-19102200	Weak transcription	Gastric	stomach
19	chr9:19079200-19099600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:19079400-19096400	Strong transcription	Dnd41	blood
21	chr9:19079600-19101200	Weak transcription	Ovary	ovary
22	chr9:19081400-19097200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:19083800-19096200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr9:19084000-19096400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:19085000-19096600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:19085000-19096800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:19085400-19101200	Weak transcription	Colonic Mucosa	Colon
28	chr9:19086000-19096400	Strong transcription	Liver	Liver
29	chr9:19086000-19096600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr9:19086400-19096800	Strong transcription	Fetal Intestine Large	intestine
31	chr9:19086600-19102200	Weak transcription	Aorta	Aorta
32	chr9:19086800-19096000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr9:19087000-19096600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr9:19088200-19096600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:19088800-19096200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:19089000-19096600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:19089200-19096400	Strong transcription	Hela-S3	cervix
38	chr9:19089200-19096400	Strong transcription	Osteobl	bone
39	chr9:19089400-19096200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:19089400-19096200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:19089600-19097000	Strong transcription	HUVEC	blood vessel
42	chr9:19089600-19102000	Weak transcription	HSMMtube	muscle
43	chr9:19089800-19101800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:19090000-19101200	Weak transcription	Right Atrium	heart
45	chr9:19090200-19101200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:19090400-19096600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:19091200-19101200	Weak transcription	Esophagus	oesophagus
48	chr9:19091600-19097000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr9:19091600-19097000	Strong transcription	NHDF-Ad	bronchial
50	chr9:19091600-19099600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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