Variant report

Variant	rs28399690
Chromosome Location	chr9:137005460-137005461
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	chr9:137005377-137005883	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:137003283..137007180-chr9:137027026..137030232,3	K562	blood:

Variant related genes	Relation type
ENSG00000273249	TF binding region
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]
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]
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	chr9:137002400-137005600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:137002400-137006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:137002400-137016200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:137002600-137005800	Genic enhancers	Fetal Stomach	stomach
5	chr9:137003200-137005600	Genic enhancers	Fetal Muscle Trunk	muscle
6	chr9:137003200-137005800	Genic enhancers	Fetal Muscle Leg	muscle
7	chr9:137003200-137024200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:137003600-137007600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:137003600-137024800	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr9:137003800-137007000	Weak transcription	Stomach Mucosa	stomach
11	chr9:137004000-137005800	Weak transcription	NH-A	brain
12	chr9:137004000-137017400	Strong transcription	HUVEC	blood vessel
13	chr9:137004000-137024000	Strong transcription	A549	lung
14	chr9:137004000-137024800	Strong transcription	Primary T cells from cord blood	blood
15	chr9:137004200-137005600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:137004200-137005600	Weak transcription	Colonic Mucosa	Colon
17	chr9:137004200-137006600	Weak transcription	Fetal Kidney	kidney
18	chr9:137004200-137007400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:137004200-137015800	Weak transcription	Fetal Heart	heart
20	chr9:137004200-137016000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:137004200-137024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr9:137004200-137024800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:137004200-137024800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr9:137004200-137025000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:137004200-137025000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr9:137004200-137026000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:137004400-137005600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:137004400-137005800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:137004400-137006000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr9:137004400-137010800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:137004400-137011800	Weak transcription	Small Intestine	intestine
32	chr9:137004400-137013600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:137004400-137014200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:137004400-137024800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:137004400-137025800	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr9:137004400-137025800	Strong transcription	Fetal Thymus	thymus
37	chr9:137004600-137005600	Weak transcription	Brain Angular Gyrus	brain
38	chr9:137004600-137005600	Weak transcription	Fetal Brain Male	brain
39	chr9:137004600-137005800	Weak transcription	NHDF-Ad	bronchial
40	chr9:137004600-137006200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:137004600-137006200	Weak transcription	HSMMtube	muscle
42	chr9:137004600-137007000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr9:137004600-137009200	Weak transcription	Psoas Muscle	Psoas
44	chr9:137004600-137010400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:137004600-137010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr9:137004600-137010800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:137004600-137011600	Strong transcription	HMEC	breast
48	chr9:137004600-137011600	Strong transcription	NHEK	skin
49	chr9:137004600-137015000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr9:137004600-137016200	Strong transcription	Spleen	Spleen

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