Variant report

Variant	rs236321
Chromosome Location	chr1:94055890-94055891
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2295330	0.80[CHB][hapmap]
rs236322	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	0.94[EUR][1000 genomes]
rs236326	0.91[EUR][1000 genomes]
rs236329	0.91[EUR][1000 genomes]
rs236330	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs236331	0.90[CHB][hapmap]
rs236332	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs236333	0.92[EUR][1000 genomes]
rs236335	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs3767975	0.90[CHB][hapmap]
rs3767976	0.91[CEU][hapmap];0.80[CHB][hapmap]
rs3767977	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs6661488	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs6674143	0.80[CHB][hapmap]
rs6692801	0.94[EUR][1000 genomes]
rs7516400	0.86[AMR][1000 genomes];0.95[EUR][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
rs236321	EPHX4	cis	cerebellum	SCAN
rs236321	BCAR3	cis	parietal	SCAN

Chromatin state (count:105 , 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	chr1:94050000-94056200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:94050000-94059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:94050800-94057800	Weak transcription	Small Intestine	intestine
14	chr1:94050800-94059200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:94051000-94056800	Weak transcription	Fetal Thymus	thymus
16	chr1:94051200-94057200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:94051200-94057200	Weak transcription	Fetal Kidney	kidney
18	chr1:94051400-94057600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:94051800-94056400	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr1:94052000-94056000	Strong transcription	Fetal Lung	lung
21	chr1:94052000-94056400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:94052000-94056800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:94052000-94057400	Weak transcription	Colonic Mucosa	Colon
24	chr1:94052200-94056000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:94052400-94057600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:94053000-94058000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:94053000-94058000	Strong transcription	NHEK	skin
28	chr1:94053200-94058200	Strong transcription	NHDF-Ad	bronchial
29	chr1:94053400-94056000	Strong transcription	Ovary	ovary
30	chr1:94053400-94056000	Genic enhancers	HUVEC	blood vessel
31	chr1:94053400-94057600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr1:94053600-94058000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:94053600-94058000	Weak transcription	Right Atrium	heart
34	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr1:94053800-94056800	Weak transcription	Pancreas	Pancrea
36	chr1:94054000-94057000	Weak transcription	Thymus	Thymus
37	chr1:94054200-94056800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:94054200-94057000	Strong transcription	Osteobl	bone
39	chr1:94054200-94057200	Strong transcription	Placenta	Placenta
40	chr1:94054200-94057400	Strong transcription	Hela-S3	cervix
41	chr1:94054200-94058200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:94054200-94058400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:94054600-94056200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:94054600-94056200	Strong transcription	NH-A	brain
46	chr1:94054600-94057200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:94054600-94057600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:94054600-94058400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
50	chr1:94054800-94056000	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links