Variant report

Variant	rs236322
Chromosome Location	chr1:94056279-94056280
allele	G/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	chr1:94056214-94056492	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94054713..94056321-chr11:62608200..62610425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224093	TF binding region
BCAR3	TF binding region
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17110124	0.98[ASN][1000 genomes]
rs2281474	0.91[ASN][1000 genomes]
rs2295330	0.90[CHB][hapmap]
rs236321	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs236323	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236326	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236329	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236331	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs236332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236333	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs236335	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs3767973	0.89[ASN][1000 genomes]
rs3767975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs3767976	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs3767977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57012808	0.91[ASN][1000 genomes]
rs57466479	0.89[ASN][1000 genomes]
rs57914444	0.89[ASN][1000 genomes]
rs59777284	0.89[ASN][1000 genomes]
rs6661488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671749	0.95[ASN][1000 genomes]
rs6674143	0.90[CHB][hapmap]
rs6692801	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516400	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518795	0.94[ASN][1000 genomes]
rs7519939	0.95[ASN][1000 genomes]
rs7524368	0.89[ASN][1000 genomes]
rs7551964	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236322	EPHX4	cis	cerebellum	SCAN
rs236322	BCAR3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:94043000-94058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:94046600-94058200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:94049600-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:94050000-94059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:94050800-94057800	Weak transcription	Small Intestine	intestine
13	chr1:94050800-94059200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:94051000-94056800	Weak transcription	Fetal Thymus	thymus
15	chr1:94051200-94057200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:94051200-94057200	Weak transcription	Fetal Kidney	kidney
17	chr1:94051400-94057600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:94051800-94056400	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr1:94052000-94056400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:94052000-94056800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:94052000-94057400	Weak transcription	Colonic Mucosa	Colon
22	chr1:94052400-94057600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:94053000-94058000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:94053000-94058000	Strong transcription	NHEK	skin
25	chr1:94053200-94058200	Strong transcription	NHDF-Ad	bronchial
26	chr1:94053400-94057600	Strong transcription	Stomach Smooth Muscle	stomach
27	chr1:94053600-94058000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:94053600-94058000	Weak transcription	Right Atrium	heart
29	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr1:94053800-94056800	Weak transcription	Pancreas	Pancrea
31	chr1:94054000-94057000	Weak transcription	Thymus	Thymus
32	chr1:94054200-94056800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:94054200-94057000	Strong transcription	Osteobl	bone
34	chr1:94054200-94057200	Strong transcription	Placenta	Placenta
35	chr1:94054200-94057400	Strong transcription	Hela-S3	cervix
36	chr1:94054200-94058200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:94054200-94058400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:94054600-94057200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:94054600-94057600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:94054600-94058400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
43	chr1:94054800-94057200	Weak transcription	Esophagus	oesophagus
44	chr1:94054800-94057200	Weak transcription	Psoas Muscle	Psoas
45	chr1:94054800-94057200	Weak transcription	Spleen	Spleen
46	chr1:94054800-94057400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:94055000-94057200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:94055000-94057200	Strong transcription	Adipose Nuclei	Adipose
49	chr1:94055000-94057200	Weak transcription	Right Ventricle	heart
50	chr1:94055000-94057200	Strong transcription	Skeletal Muscle Male	skeletal muscle

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