Variant report

Variant	rs28708401
Chromosome Location	chr9:137004279-137004280
allele	A/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	POLR2A	chr9:137003273-137004552	HepG2	liver:	n/a	n/a
2	CTCF	chr9:137004260-137004410	AG10803	skin:	n/a	n/a
3	FOXP2	chr9:137004255-137004558	SK-N-MC	brain:	n/a	n/a
4	CEBPB	chr9:137004186-137004677	IMR90	lung:	n/a	chr9:137004481-137004492
5	CEBPB	chr9:137004215-137004596	MCF-7	breast:	n/a	chr9:137004481-137004492
6	POLR2A	chr9:137003617-137004304	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr9:137004174-137004781	A549	lung:	n/a	chr9:137004481-137004492

No.	Distal block	Cell Line	Cell type
1	chr9:136932690..136935080-chr9:137003441..137005032,2	MCF-7	breast:
2	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
3	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:

Variant related genes	Relation type
ENSG00000273249	TF binding region
WDR5	TF binding region
ENSG00000169925	Chromatin interaction
ENSG00000221676	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs28360858	1.00[EUR][1000 genomes]
rs28377785	1.00[AFR][1000 genomes]
rs28399690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28401385	1.00[EUR][1000 genomes]
rs28412245	1.00[EUR][1000 genomes]
rs28421319	1.00[AFR][1000 genomes]
rs28425680	1.00[AFR][1000 genomes]
rs28436125	1.00[AFR][1000 genomes]
rs28440102	1.00[EUR][1000 genomes]
rs28452481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28473171	1.00[EUR][1000 genomes]
rs28479377	1.00[EUR][1000 genomes]
rs28491791	1.00[EUR][1000 genomes]
rs28507057	1.00[EUR][1000 genomes]
rs28562287	1.00[AFR][1000 genomes]
rs28562957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28579703	1.00[EUR][1000 genomes]
rs28594106	1.00[AFR][1000 genomes]
rs28620240	1.00[EUR][1000 genomes]
rs28626085	1.00[AFR][1000 genomes]
rs28687115	1.00[AFR][1000 genomes]
rs28705689	1.00[EUR][1000 genomes]
rs28710163	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28712382	1.00[EUR][1000 genomes]
rs28714237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28740804	1.00[EUR][1000 genomes]
rs28758854	1.00[EUR][1000 genomes]
rs28759311	1.00[EUR][1000 genomes]
rs34022301	1.00[AFR][1000 genomes]
rs34079254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34194763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34473303	1.00[EUR][1000 genomes]
rs34546899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34607253	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34646496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34861636	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34929179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35209649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35322411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35370793	1.00[AFR][1000 genomes]
rs35387289	1.00[EUR][1000 genomes]
rs35419030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35448798	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35487246	0.84[EUR][1000 genomes]
rs35489314	1.00[EUR][1000 genomes]
rs35504753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35511305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35709000	1.00[EUR][1000 genomes]
rs35726748	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35874066	1.00[AFR][1000 genomes]
rs35924689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35962164	1.00[AFR][1000 genomes]
rs36029182	1.00[AFR][1000 genomes]
rs71483222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71505283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71505284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 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	chr9:137001600-137004600	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr9:137001800-137004400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:137002000-137004800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:137002200-137004400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:137002400-137004400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:137002400-137004400	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr9:137002400-137004400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr9:137002400-137004400	Enhancers	Small Intestine	intestine
9	chr9:137002400-137004600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr9:137002400-137004600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:137002400-137004600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:137002400-137004600	Enhancers	Esophagus	oesophagus
13	chr9:137002400-137004600	Enhancers	Ovary	ovary
14	chr9:137002400-137004600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr9:137002400-137004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:137002400-137004800	Enhancers	Adipose Nuclei	Adipose
17	chr9:137002400-137004800	Enhancers	Left Ventricle	heart
18	chr9:137002400-137005600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:137002400-137006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:137002400-137016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr9:137002600-137004400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:137002600-137004400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:137002600-137004400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr9:137002600-137004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:137002600-137004400	Enhancers	Right Ventricle	heart
26	chr9:137002600-137004600	Enhancers	Brain Substantia Nigra	brain
27	chr9:137002600-137004800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr9:137002600-137005000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:137002600-137005000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:137002600-137005000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:137002600-137005000	Enhancers	Pancreas	Pancrea
32	chr9:137002600-137005200	Genic enhancers	Fetal Intestine Small	intestine
33	chr9:137002600-137005800	Genic enhancers	Fetal Stomach	stomach
34	chr9:137002800-137004600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr9:137002800-137004800	Enhancers	Colon Smooth Muscle	Colon
36	chr9:137003000-137004600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:137003000-137004600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr9:137003000-137004600	Enhancers	Right Atrium	heart
39	chr9:137003000-137005200	Weak transcription	K562	blood
40	chr9:137003200-137004400	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr9:137003200-137004400	Genic enhancers	Fetal Intestine Large	intestine
42	chr9:137003200-137004600	Enhancers	Liver	Liver
43	chr9:137003200-137004600	Flanking Active TSS	Fetal Brain Female	brain
44	chr9:137003200-137004600	Enhancers	Psoas Muscle	Psoas
45	chr9:137003200-137004600	Transcr. at gene 5' and 3'	Hela-S3	cervix
46	chr9:137003200-137004800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr9:137003200-137004800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr9:137003200-137005600	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr9:137003200-137005800	Genic enhancers	Fetal Muscle Leg	muscle
50	chr9:137003200-137024200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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