Variant report

Variant	rs296892
Chromosome Location	chr9:86597806-86597807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr9:86597709-86597841	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
2	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
3	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
4	chr9:86596431..86597964-chr9:86790384..86792267,2	MCF-7	breast:
5	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:

No data

Variant related genes	Relation type
HNRNPK	TF binding region
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10124390	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10125673	0.88[ASN][1000 genomes]
rs10780639	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10780640	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868071	0.80[YRI][hapmap]
rs10868077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868079	0.83[CHB][hapmap]
rs11792634	0.81[CHB][hapmap]
rs12004439	0.82[EUR][1000 genomes]
rs12006540	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12551039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13296528	0.81[YRI][hapmap]
rs1572030	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1572031	0.87[CHB][hapmap]
rs177042	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831757	0.81[YRI][hapmap]
rs1982151	0.89[YRI][hapmap]
rs2065516	0.87[CHB][hapmap]
rs2780103	0.82[YRI][hapmap]
rs2780142	0.83[CHB][hapmap]
rs295274	0.83[CHB][hapmap]
rs296885	0.87[CHB][hapmap]
rs296887	0.90[YRI][hapmap]
rs296888	0.86[YRI][hapmap]
rs296889	0.89[YRI][hapmap]
rs296890	0.90[YRI][hapmap]
rs296891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs296893	0.84[YRI][hapmap]
rs4147132	0.82[YRI][hapmap]
rs4297107	0.83[CHB][hapmap]
rs4535826	0.82[YRI][hapmap]
rs4877814	0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877815	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5018100	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6559750	0.83[CHB][hapmap]
rs6559753	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6559754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6559756	0.96[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7020841	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7021189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026436	0.83[CHB][hapmap]
rs7045008	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs754144	0.87[CHB][hapmap]
rs7864367	0.93[EUR][1000 genomes]
rs7869321	0.81[YRI][hapmap]
rs7869387	0.87[CHB][hapmap]
rs7875011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875242	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875289	0.87[CHB][hapmap]
rs796000	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796002	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314723	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86593000-86598600	Active TSS	GM12878-XiMat	blood
2	chr9:86594200-86598400	Active TSS	K562	blood
3	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
4	chr9:86596600-86601800	Weak transcription	Pancreas	Pancrea
5	chr9:86596600-86603200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:86596600-86610600	Weak transcription	Esophagus	oesophagus
7	chr9:86596600-86613400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:86596600-86613800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:86596600-86616000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:86596600-86617000	Weak transcription	Lung	lung
11	chr9:86596600-86618200	Weak transcription	Ovary	ovary
12	chr9:86596600-86619600	Weak transcription	Gastric	stomach
13	chr9:86596800-86598000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr9:86596800-86598000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr9:86596800-86601200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr9:86596800-86601200	Weak transcription	Liver	Liver
17	chr9:86596800-86601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:86596800-86601800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr9:86596800-86601800	Weak transcription	Left Ventricle	heart
20	chr9:86596800-86601800	Weak transcription	HSMM	muscle
21	chr9:86596800-86602000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr9:86596800-86603200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:86596800-86603200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:86596800-86603200	Weak transcription	Fetal Thymus	thymus
25	chr9:86596800-86605400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr9:86596800-86606600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:86596800-86613200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:86596800-86614400	Weak transcription	HSMMtube	muscle
29	chr9:86596800-86616000	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:86596800-86616200	Weak transcription	Brain Angular Gyrus	brain
31	chr9:86596800-86616200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:86596800-86619600	Weak transcription	Small Intestine	intestine
33	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:86597000-86598000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:86597000-86598000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr9:86597000-86598200	Enhancers	Fetal Stomach	stomach
38	chr9:86597000-86598600	Flanking Active TSS	Dnd41	blood
39	chr9:86597000-86598800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:86597000-86598800	Enhancers	Hela-S3	cervix
41	chr9:86597000-86600400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr9:86597000-86600600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr9:86597000-86601000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr9:86597000-86601200	Weak transcription	Osteobl	bone
45	chr9:86597000-86601400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr9:86597000-86602000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:86597000-86602800	Weak transcription	Fetal Intestine Small	intestine
48	chr9:86597000-86603200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr9:86597000-86603200	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:86597000-86603400	Weak transcription	Fetal Intestine Large	intestine

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