Variant report

Variant	rs9286999
Chromosome Location	chr1:226494515-226494516
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226488992..226494999-chr1:226495379..226497863,6	MCF-7	breast:
2	chr1:226480171..226482069-chr1:226492997..226494940,2	K562	blood:
3	chr1:226494508..226498225-chr1:226504604..226509002,8	K562	blood:
4	chr1:226483787..226486483-chr1:226492204..226494854,3	K562	blood:
5	chr1:226490285..226492434-chr1:226493434..226496087,2	MCF-7	breast:
6	chr1:226494405..226496827-chr1:226598001..226600824,2	K562	blood:

Variant related genes	Relation type
ENSG00000270287	Chromatin interaction
ENSG00000236994	Chromatin interaction
ENSG00000238545	Chromatin interaction
ENSG00000183814	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10753418	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10799340	0.87[MEX][hapmap]
rs12136759	0.87[MEX][hapmap]
rs1219652	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1219659	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1361559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2199501	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2306119	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs3008190	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs3008192	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6668540	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6703375	0.82[AFR][1000 genomes]
rs7367845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7368170	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9629826	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv517107	chr1:226375267-226508645	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv873233	chr1:226385623-226508645	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv832770	chr1:226465130-226655512	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9286999	JMJD4	cis	parietal	SCAN
rs9286999	ACBD3	Cis_1M	lymphoblastoid	RTeQTL
rs9286999	PARP1	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226415800-226495400	Weak transcription	Liver	Liver
2	chr1:226416200-226495600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:226434200-226496000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:226436800-226496000	Weak transcription	Esophagus	oesophagus
5	chr1:226448200-226495600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:226450800-226495600	Weak transcription	Adipose Nuclei	Adipose
7	chr1:226452000-226496000	Weak transcription	Fetal Lung	lung
8	chr1:226456600-226496000	Weak transcription	Brain Angular Gyrus	brain
9	chr1:226457000-226495600	Weak transcription	Fetal Kidney	kidney
10	chr1:226457200-226495600	Weak transcription	NHDF-Ad	bronchial
11	chr1:226457200-226495600	Weak transcription	NHLF	lung
12	chr1:226457400-226495800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:226460800-226496000	Weak transcription	Gastric	stomach
14	chr1:226460800-226496000	Weak transcription	Pancreas	Pancrea
15	chr1:226461200-226496200	Weak transcription	Aorta	Aorta
16	chr1:226467800-226496000	Weak transcription	Brain Substantia Nigra	brain
17	chr1:226468600-226495600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:226469600-226495800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:226471000-226496000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:226472400-226495400	Weak transcription	NH-A	brain
21	chr1:226472600-226496000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:226473000-226495800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:226474600-226495400	Weak transcription	HSMM	muscle
24	chr1:226474800-226496200	Weak transcription	Small Intestine	intestine
25	chr1:226475400-226495400	Weak transcription	HMEC	breast
26	chr1:226477400-226494800	Weak transcription	HepG2	liver
27	chr1:226479000-226495400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:226479000-226495800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:226479000-226495800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:226480000-226495800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:226480200-226496000	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:226480800-226496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:226481600-226495400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:226481800-226496000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:226482000-226494800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:226483600-226495400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:226483800-226495400	Weak transcription	Primary T cells from cord blood	blood
38	chr1:226484200-226495400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:226484200-226495600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:226484200-226495600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:226484800-226495600	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:226484800-226495800	Weak transcription	Colon Smooth Muscle	Colon
43	chr1:226484800-226496000	Weak transcription	Ovary	ovary
44	chr1:226485000-226495400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:226485000-226495400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:226485000-226495400	Weak transcription	NHEK	skin
47	chr1:226485000-226495800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:226485000-226495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:226485200-226495400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:226485200-226495800	Weak transcription	Fetal Intestine Large	intestine

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