Variant report

Variant	rs4978510
Chromosome Location	chr9:115643795-115643796
allele	C/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	FOS	chr9:115643733-115644024	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr9:115643494-115643983	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr9:115643723-115644024	MCF10A-Er-Src	breast:	n/a	n/a
4	EGR1	chr9:115643738-115643936	K562	blood:	n/a	chr9:115643846-115643859 chr9:115643852-115643859
5	EGR1	chr9:115643514-115644216	HCT-116	colon:	n/a	chr9:115643846-115643859 chr9:115643852-115643859
6	EGR1	chr9:115643574-115644150	HCT-116	colon:	n/a	chr9:115643846-115643859 chr9:115643852-115643859
7	USF1	chr9:115643562-115643977	ECC-1	luminal epithelium:	n/a	n/a
8	E2F4	chr9:115643627-115643933	MCF10A-Er-Src	breast:	n/a	chr9:115643633-115643642 chr9:115643634-115643641 chr9:115643633-115643645 chr9:115643634-115643641 chr9:115643630-115643644 chr9:115643634-115643641
9	MAX	chr9:115643388-115644022	ECC-1	luminal epithelium:	n/a	n/a
10	FOS	chr9:115643716-115644107	MCF10A-Er-Src	breast:	n/a	n/a
11	USF1	chr9:115643543-115643941	ECC-1	luminal epithelium:	n/a	n/a
12	MYC	chr9:115643729-115644101	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr9:115643703-115644076	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr9:115643768-115643968	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115634993..115639011-chr9:115640065..115646725,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271631	TF binding region

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10115576	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs10115711	0.82[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124260	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs10124939	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs10124979	0.82[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733594	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs10733598	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10733599	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739370	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs10739373	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs10739374	1.00[ASN][1000 genomes]
rs10739376	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10739378	1.00[CEU][hapmap]
rs10739380	0.83[EUR][1000 genomes]
rs10759590	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10759603	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10759604	1.00[ASN][1000 genomes]
rs1158331	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324931	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs1361720	0.85[CEU][hapmap]
rs1418409	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1475293	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs1539338	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1570754	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693411	1.00[ASN][1000 genomes]
rs1711746	1.00[ASN][1000 genomes]
rs1711747	0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1832890	1.00[ASN][1000 genomes]
rs1891402	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1891403	0.85[CEU][hapmap];0.94[GIH][hapmap]
rs2025544	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051018	1.00[ASN][1000 genomes]
rs2147643	1.00[ASN][1000 genomes]
rs2147646	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153837	0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs2182048	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185769	1.00[ASN][1000 genomes]
rs2645985	1.00[ASN][1000 genomes]
rs2645993	0.85[CEU][hapmap]
rs2645994	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs2796025	1.00[ASN][1000 genomes]
rs2796028	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs2796031	1.00[ASN][1000 genomes]
rs2796035	1.00[ASN][1000 genomes]
rs4246892	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4304397	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs4360356	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549852	1.00[ASN][1000 genomes]
rs4978507	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4978511	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4979153	0.85[CEU][hapmap]
rs4979154	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979155	1.00[ASN][1000 genomes]
rs4979157	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979165	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979170	1.00[CEU][hapmap]
rs4979171	0.91[EUR][1000 genomes]
rs4979183	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979184	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979186	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477959	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs700122	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7026450	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030795	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7038684	1.00[ASN][1000 genomes]
rs7040954	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041965	1.00[ASN][1000 genomes]
rs7047914	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859175	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7868830	0.85[CEU][hapmap]
rs7869100	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786961	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs786965	1.00[ASN][1000 genomes]
rs786966	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs786967	1.00[ASN][1000 genomes]
rs786968	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs786969	1.00[ASN][1000 genomes]
rs786972	1.00[ASN][1000 genomes]
rs786973	1.00[ASN][1000 genomes]
rs786977	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs7872628	1.00[ASN][1000 genomes]
rs787271	0.85[CEU][hapmap];0.94[GIH][hapmap]
rs787274	0.94[GIH][hapmap]
rs787276	0.85[CEU][hapmap]
rs787278	1.00[ASN][1000 genomes]
rs787280	0.85[CEU][hapmap];0.94[GIH][hapmap]
rs787281	1.00[ASN][1000 genomes]
rs787284	0.85[CEU][hapmap]
rs787285	1.00[ASN][1000 genomes]
rs787286	1.00[ASN][1000 genomes]
rs787287	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs787291	1.00[ASN][1000 genomes]
rs787294	0.85[CEU][hapmap]
rs787295	0.85[CEU][hapmap];0.94[GIH][hapmap]
rs787296	1.00[ASN][1000 genomes]
rs787297	0.85[CEU][hapmap];0.94[GIH][hapmap]
rs787298	0.85[CEU][hapmap]
rs787299	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs787301	0.85[CEU][hapmap];0.93[GIH][hapmap]
rs787302	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs787303	1.00[ASN][1000 genomes]
rs7873289	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs813101	0.85[CEU][hapmap]
rs885387	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs912662	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409123	0.85[CEU][hapmap]
rs947609	1.00[ASN][1000 genomes]
rs980345	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4978510	TSCOT	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115615600-115646400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:115624200-115652600	Weak transcription	Fetal Heart	heart
3	chr9:115625800-115645200	Weak transcription	Thymus	Thymus
4	chr9:115626400-115650800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:115627000-115647000	Weak transcription	Colonic Mucosa	Colon
6	chr9:115627600-115646800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:115630600-115646400	Weak transcription	Fetal Lung	lung
8	chr9:115630600-115647200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:115630800-115646400	Weak transcription	Placenta	Placenta
10	chr9:115631200-115646400	Weak transcription	Fetal Kidney	kidney
11	chr9:115631400-115643800	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:115631800-115646400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:115631800-115652200	Weak transcription	Gastric	stomach
14	chr9:115632200-115644800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:115633000-115645800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr9:115633000-115646400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:115633000-115652600	Weak transcription	Left Ventricle	heart
18	chr9:115633200-115646400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:115633200-115652400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:115633200-115652400	Weak transcription	Right Ventricle	heart
21	chr9:115633400-115646800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:115633400-115648200	Weak transcription	Esophagus	oesophagus
23	chr9:115633400-115649200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr9:115633600-115644400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr9:115633800-115652600	Weak transcription	Liver	Liver
26	chr9:115634600-115646400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:115634800-115646400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:115634800-115651800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:115635000-115650800	Weak transcription	Fetal Thymus	thymus
30	chr9:115635600-115649000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr9:115636000-115648600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr9:115636600-115646400	Weak transcription	NHDF-Ad	bronchial
33	chr9:115637400-115644000	Strong transcription	Fetal Intestine Small	intestine
34	chr9:115638000-115644000	Strong transcription	Fetal Muscle Leg	muscle
35	chr9:115638200-115644000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:115638200-115647000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:115638600-115650000	Weak transcription	Fetal Brain Female	brain
38	chr9:115639000-115644000	Strong transcription	Aorta	Aorta
39	chr9:115639000-115644200	Strong transcription	Brain Hippocampus Middle	brain
40	chr9:115640200-115643800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:115640400-115644800	Weak transcription	Psoas Muscle	Psoas
42	chr9:115640800-115647000	Weak transcription	Primary T cells from cord blood	blood
43	chr9:115641000-115646400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr9:115641600-115643800	Strong transcription	Lung	lung
45	chr9:115641600-115644000	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr9:115641800-115644200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr9:115642200-115644800	Strong transcription	Fetal Stomach	stomach
48	chr9:115642600-115644000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr9:115642800-115644000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:115642800-115644000	Strong transcription	Fetal Intestine Large	intestine

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