Variant report

Variant	rs28562957
Chromosome Location	chr9:137004651-137004652
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	CEBPB	chr9:137004186-137004677	IMR90	lung:	n/a	chr9:137004481-137004492
2	CEBPB	chr9:137004298-137004653	A549	lung:	n/a	chr9:137004481-137004492
3	CEBPB	chr9:137004309-137004683	K562	blood:	n/a	chr9:137004481-137004492
4	CEBPB	chr9:137004174-137004781	A549	lung:	n/a	chr9:137004481-137004492
5	CEBPB	chr9:137004287-137004670	HepG2	liver:	n/a	chr9:137004481-137004492
6	CTCF	chr9:137004520-137004670	NHLF	lung:	n/a	n/a
7	CEBPB	chr9:137004310-137004668	Hela-S3	cervix:	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]
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]
rs28708401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137002000-137004800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:137002400-137004800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:137002400-137004800	Enhancers	Adipose Nuclei	Adipose
4	chr9:137002400-137004800	Enhancers	Left Ventricle	heart
5	chr9:137002400-137005600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:137002400-137006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:137002400-137016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:137002600-137004800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr9:137002600-137005000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:137002600-137005000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:137002600-137005000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr9:137002600-137005000	Enhancers	Pancreas	Pancrea
13	chr9:137002600-137005200	Genic enhancers	Fetal Intestine Small	intestine
14	chr9:137002600-137005800	Genic enhancers	Fetal Stomach	stomach
15	chr9:137002800-137004800	Enhancers	Colon Smooth Muscle	Colon
16	chr9:137003000-137005200	Weak transcription	K562	blood
17	chr9:137003200-137004800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:137003200-137004800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr9:137003200-137005600	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr9:137003200-137005800	Genic enhancers	Fetal Muscle Leg	muscle
21	chr9:137003200-137024200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:137003600-137004800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:137003600-137005200	Weak transcription	Primary B cells from cord blood	blood
24	chr9:137003600-137007600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:137003600-137024800	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr9:137003800-137004800	Enhancers	Brain Germinal Matrix	brain
27	chr9:137003800-137005000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:137003800-137005000	Weak transcription	Placenta	Placenta
29	chr9:137003800-137005000	Weak transcription	Thymus	Thymus
30	chr9:137003800-137005200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:137003800-137007000	Weak transcription	Stomach Mucosa	stomach
32	chr9:137004000-137005000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr9:137004000-137005800	Weak transcription	NH-A	brain
34	chr9:137004000-137017400	Strong transcription	HUVEC	blood vessel
35	chr9:137004000-137024000	Strong transcription	A549	lung
36	chr9:137004000-137024800	Strong transcription	Primary T cells from cord blood	blood
37	chr9:137004200-137004800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr9:137004200-137004800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr9:137004200-137004800	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr9:137004200-137005000	Enhancers	Fetal Lung	lung
41	chr9:137004200-137005200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:137004200-137005200	Genic enhancers	Lung	lung
43	chr9:137004200-137005600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:137004200-137005600	Weak transcription	Colonic Mucosa	Colon
45	chr9:137004200-137006600	Weak transcription	Fetal Kidney	kidney
46	chr9:137004200-137007400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr9:137004200-137015800	Weak transcription	Fetal Heart	heart
48	chr9:137004200-137016000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr9:137004200-137024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr9:137004200-137024800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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