Variant report

Variant	rs7030031
Chromosome Location	chr9:117879212-117879213
allele	A/C
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	POLR2A	chr9:117858058-117881674	U87	brain:	n/a	n/a
2	GATA3	chr9:117878850-117879494	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr9:117877891-117881556	U87	brain:	n/a	n/a
4	GATA3	chr9:117876789-117879555	SK-N-SH	brain:	n/a	chr9:117878767-117878775
5	POLR2A	chr9:117877249-117881760	IMR90	lung:	n/a	n/a
6	TCF12	chr9:117876852-117879384	SK-N-SH	brain:	n/a	chr9:117876898-117876905
7	FOS	chr9:117878916-117879229	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr9:117877221-117881586	U87	brain:	n/a	n/a
9	PBX3	chr9:117878210-117879371	SK-N-SH	brain:	n/a	n/a
10	MYC	chr9:117878952-117879250	MCF10A-Er-Src	breast:	n/a	n/a
11	RCOR1	chr9:117877222-117879859	IMR90	lung:	n/a	n/a
12	EP300	chr9:117877875-117879433	SK-N-SH	brain:	n/a	chr9:117879156-117879172
13	POLR2A	chr9:117878956-117879305	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr9:117878936-117879774	ECC-1	luminal epithelium:	n/a	n/a
15	TCF12	chr9:117876174-117879494	SK-N-SH	brain:	n/a	chr9:117876898-117876905
16	STAT3	chr9:117878931-117879223	MCF10A-Er-Src	breast:	n/a	chr9:117879166-117879178
17	POLR2A	chr9:117876849-117879682	SK-N-SH	brain:	n/a	n/a
18	GATA3	chr9:117878994-117879264	T-47D	breast:	n/a	n/a
19	STAT3	chr9:117879019-117879295	MCF10A-Er-Src	breast:	n/a	chr9:117879166-117879178
20	POLR2A	chr9:117863693-117881740	U87	brain:	n/a	n/a
21	NFIC	chr9:117876700-117879564	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10982546	1.00[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1335330	0.88[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1335334	0.84[JPT][hapmap]
rs1414138	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs1537721	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1537722	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1537727	0.92[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1537728	0.92[CEU][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2094941	0.92[CEU][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2992148	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4246907	0.92[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4978618	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4979508	0.84[JPT][hapmap]
rs884789	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[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	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117876000-117879400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:117876400-117880200	Enhancers	Hela-S3	cervix
3	chr9:117877000-117879400	Flanking Active TSS	NH-A	brain
4	chr9:117877200-117881400	Active TSS	Fetal Kidney	kidney
5	chr9:117877400-117879400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:117877400-117879800	Flanking Active TSS	Osteobl	bone
7	chr9:117877600-117879800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:117877600-117880200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr9:117877600-117881600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
10	chr9:117877800-117879600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr9:117877800-117880000	Active TSS	Fetal Brain Female	brain
12	chr9:117878000-117880200	Active TSS	Stomach Smooth Muscle	stomach
13	chr9:117878000-117881600	Active TSS	Colon Smooth Muscle	Colon
14	chr9:117878200-117880200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:117878200-117880400	Active TSS	Rectal Smooth Muscle	rectum
16	chr9:117878200-117880800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:117878200-117881000	Active TSS	NHLF	lung
18	chr9:117878200-117881400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr9:117878200-117881600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr9:117878200-117881600	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr9:117878400-117879800	Flanking Active TSS	HMEC	breast
22	chr9:117878400-117880000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:117878400-117880200	Active TSS	Brain Germinal Matrix	brain
24	chr9:117878400-117880600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:117878400-117881000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:117878600-117879800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:117878600-117879800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
28	chr9:117878600-117879800	Flanking Active TSS	NHEK	skin
29	chr9:117878600-117880000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:117878600-117880000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:117878600-117880200	Active TSS	Brain Anterior Caudate	brain
32	chr9:117878600-117880200	Bivalent/Poised TSS	Fetal Brain Male	brain
33	chr9:117878600-117880200	Active TSS	Fetal Muscle Trunk	muscle
34	chr9:117878600-117880400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:117878600-117880600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
36	chr9:117878600-117880600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr9:117878600-117881400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:117878600-117881400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:117878800-117879400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr9:117878800-117879600	Flanking Active TSS	Fetal Stomach	stomach
41	chr9:117878800-117879800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr9:117878800-117880200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:117878800-117880200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr9:117878800-117880800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr9:117879000-117879400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:117879000-117879600	Active TSS	Lung	lung
47	chr9:117879000-117880000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:117879000-117880200	Active TSS	Right Ventricle	heart
49	chr9:117879000-117881400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
50	chr9:117879000-117881400	Active TSS	Cortex derived primary cultured neurospheres	brain

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