Variant report

Variant	rs296886
Chromosome Location	chr9:86592026-86592027
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	POLR2A	chr9:86592005-86597005	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
3	POLR2A	chr9:86589056-86597036	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:86591923-86592093	Hela-S3	cervix:	n/a	n/a
5	NFATC1	chr9:86592005-86592742	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:86591266-86593022	U87	brain:	n/a	n/a
7	POLR2A	chr9:86584019-86593013	HepG2	liver:	n/a	n/a
8	POLR2A	chr9:86591266-86592530	U87	brain:	n/a	n/a
9	POLR2A	chr9:86591552-86592884	A549	lung:	n/a	n/a
10	POLR2A	chr9:86592019-86592943	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:86584178-86592956	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86535076..86537991-chr9:86590146..86593000,2	K562	blood:

Variant related genes	Relation type
RMI1	TF binding region
HNRNPK	TF binding region
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10114889	0.82[CEU][hapmap]
rs10780645	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap]
rs12344699	0.89[YRI][hapmap]
rs12682981	0.82[CEU][hapmap]
rs13290882	0.82[CEU][hapmap]
rs13295313	0.99[EUR][1000 genomes]
rs13296528	0.82[CEU][hapmap]
rs167203	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1831757	0.81[CEU][hapmap]
rs1982151	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs2576362	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2780103	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs28521174	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs296887	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs296888	0.87[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs296889	0.87[CEU][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs296893	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs296894	0.93[CEU][hapmap];0.84[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs3180887	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs4147132	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4147133	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs6559742	0.93[CEU][hapmap]
rs6559751	0.82[CEU][hapmap]
rs7020300	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs7033292	0.87[CEU][hapmap]
rs7853235	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap]
rs7853377	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7861065	0.84[EUR][1000 genomes]
rs7869321	0.82[CEU][hapmap]
rs796003	0.81[EUR][1000 genomes]
rs796004	0.81[EUR][1000 genomes]
rs796007	0.81[EUR][1000 genomes]
rs930340	0.93[CEU][hapmap];0.90[YRI][hapmap]
rs963459	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs296886	LOC440173	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86572200-86593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:86581200-86592200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:86581200-86592200	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:86581200-86592400	Strong transcription	Fetal Thymus	thymus
5	chr9:86581200-86593000	Strong transcription	Placenta	Placenta
6	chr9:86581400-86592200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr9:86581400-86592200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr9:86581600-86592200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:86581600-86592600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr9:86581800-86592200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:86581800-86592600	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr9:86582200-86592800	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr9:86582600-86592200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:86583800-86592600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr9:86584600-86592800	Strong transcription	Colonic Mucosa	Colon
16	chr9:86585800-86592600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:86586000-86592800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:86586600-86592600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr9:86586800-86592200	Genic enhancers	A549	lung
20	chr9:86587400-86592600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:86587400-86593000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr9:86587600-86592200	Genic enhancers	Primary T cells from cord blood	blood
23	chr9:86588400-86593000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
24	chr9:86588600-86592800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr9:86588600-86592800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr9:86588800-86592200	Weak transcription	Stomach Mucosa	stomach
27	chr9:86589000-86592200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:86589200-86593200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:86589400-86592600	Genic enhancers	Hela-S3	cervix
30	chr9:86589600-86592600	Genic enhancers	Brain Hippocampus Middle	brain
31	chr9:86589600-86593000	Genic enhancers	Brain Inferior Temporal Lobe	brain
32	chr9:86589800-86592600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr9:86589800-86592600	Genic enhancers	Brain Anterior Caudate	brain
34	chr9:86589800-86592800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr9:86590000-86592400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr9:86590000-86594400	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr9:86590200-86592400	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr9:86590400-86592800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:86590600-86592200	Strong transcription	Liver	Liver
40	chr9:86590600-86592400	Weak transcription	Aorta	Aorta
41	chr9:86590600-86592400	Weak transcription	Right Ventricle	heart
42	chr9:86590600-86592600	Strong transcription	Fetal Muscle Leg	muscle
43	chr9:86590600-86592600	Weak transcription	Right Atrium	heart
44	chr9:86590600-86592800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:86590600-86593000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr9:86590600-86593800	Weak transcription	Gastric	stomach
47	chr9:86590600-86594000	Weak transcription	Spleen	Spleen
48	chr9:86590800-86592200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:86590800-86592200	Weak transcription	Fetal Intestine Small	intestine
50	chr9:86590800-86592200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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