Variant report

Variant	rs1421139
Chromosome Location	chr9:96938862-96938863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:96935497-96946284	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:96938725-96940000	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:96938811-96939394	U87	brain:	n/a	n/a
4	POLR2A	chr9:96935486-96946923	K562	blood:	n/a	n/a
5	POLR2A	chr9:96938825-96939923	SK-N-MC	brain:	n/a	n/a
6	E2F4	chr9:96938855-96939187	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr9:96935500-96945447	A549	lung:	n/a	n/a
8	POLR2A	chr9:96938796-96940009	GM12878	blood:	n/a	n/a
9	FOXA1	chr9:96938729-96939227	HepG2	liver:	n/a	n/a
10	POLR2A	chr9:96938823-96939987	Hela-S3	cervix:	n/a	n/a
11	FOXA1	chr9:96938828-96939199	HepG2	liver:	n/a	n/a
12	FOS	chr9:96938775-96939279	HUVEC	blood vessel:	n/a	chr9:96939068-96939079
13	POLR2A	chr9:96937775-96940483	U87	brain:	n/a	n/a
14	POLR2A	chr9:96938859-96939949	GM12878	blood:	n/a	n/a
15	POLR2A	chr9:96938849-96939929	GM12892	blood:	n/a	n/a
16	POLR2A	chr9:96938624-96938942	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr9:96938818-96944848	K562	blood:	n/a	n/a
18	POLR2A	chr9:96938767-96939997	K562	blood:	n/a	n/a
19	POLR2A	chr9:96938853-96946169	Hela-S3	cervix:	n/a	n/a
20	FOXA1	chr9:96938816-96939179	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96844456..96848566-chr9:96937566..96941042,3	K562	blood:
2	chr9:96791676..96794493-chr9:96936767..96941836,4	MCF-7	breast:
3	chr9:96790406..96793524-chr9:96937356..96939962,3	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPDC1-7	chr9:96938785-96939872	NONHSAT133286
2	lnc-PTPDC1-7	chr9:96938740-96940174	ENSG00000269929.1
3	lnc-FAM22F-1	chr9:96938852-96940013	NONHSAT133295
4	lnc-FAM22F-1	chr9:96938852-96940013	NONHSAT133296

No data

Variant related genes	Relation type
MIRLET7D	TF binding region
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16909702	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16909728	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60658774	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73653440	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73653443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73653444	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73653447	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73653451	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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 miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96929800-96944800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:96930600-96943600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:96930600-96943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:96931800-96939000	Weak transcription	Fetal Brain Male	brain
7	chr9:96933400-96939000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:96933600-96939400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:96933600-96939800	Strong transcription	Hela-S3	cervix
10	chr9:96933800-96940400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:96934000-96941800	Strong transcription	Dnd41	blood
12	chr9:96934200-96939600	Enhancers	Brain Substantia Nigra	brain
13	chr9:96934200-96939800	Genic enhancers	Osteobl	bone
14	chr9:96934200-96941000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:96934400-96939800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:96934400-96942400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:96935000-96939600	Genic enhancers	HUVEC	blood vessel
18	chr9:96935000-96939800	Genic enhancers	A549	lung
19	chr9:96935200-96940600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr9:96935400-96939200	Genic enhancers	NH-A	brain
21	chr9:96935400-96939400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:96935400-96939600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:96935400-96940000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr9:96935400-96940000	Strong transcription	Fetal Muscle Trunk	muscle
25	chr9:96935400-96942200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:96935400-96942400	Strong transcription	Fetal Thymus	thymus
27	chr9:96935600-96939200	Genic enhancers	Duodenum Mucosa	Duodenum
28	chr9:96935600-96939400	Genic enhancers	Liver	Liver
29	chr9:96935600-96942400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:96935600-96942400	Genic enhancers	HepG2	liver
31	chr9:96935800-96939200	Genic enhancers	HSMM	muscle
32	chr9:96935800-96939200	Genic enhancers	NHEK	skin
33	chr9:96935800-96940000	Strong transcription	K562	blood
34	chr9:96935800-96940400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:96935800-96940400	Weak transcription	Spleen	Spleen
36	chr9:96935800-96942400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:96936000-96939200	Genic enhancers	Rectal Mucosa Donor 29	rectum
38	chr9:96936000-96940200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr9:96936000-96940400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr9:96936000-96941800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr9:96936200-96939400	Genic enhancers	Rectal Mucosa Donor 31	rectum
42	chr9:96936600-96939400	Genic enhancers	HMEC	breast
43	chr9:96936600-96939600	Genic enhancers	Adipose Nuclei	Adipose
44	chr9:96936800-96939000	Weak transcription	Lung	lung
45	chr9:96936800-96945200	Weak transcription	Fetal Intestine Small	intestine
46	chr9:96937000-96939000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr9:96937000-96939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:96937000-96939000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr9:96937000-96939000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:96937000-96939000	Weak transcription	Esophagus	oesophagus

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