Variant report

Variant	rs3599
Chromosome Location	chrX:154467737-154467738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:154462893..154464786-chrX:154466274..154467936,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155959	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1128863	1.00[CEU][hapmap];0.87[TSI][hapmap]
rs12387365	1.00[CEU][hapmap]
rs17052027	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs5940367	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5940453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5987093	1.00[CEU][hapmap];0.87[TSI][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	nsv916671	chrX:154418093-154560374	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv532966	chrX:154418093-154721378	Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv29972	chrX:154418093-154929412	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv532965	chrX:154418093-155226096	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv532967	chrX:154418093-155252027	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534387	chrX:154455491-154560375	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:154445600-154467800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chrX:154445600-154471800	Weak transcription	Aorta	Aorta
3	chrX:154446200-154468000	Weak transcription	Brain Substantia Nigra	brain
4	chrX:154446200-154469800	Weak transcription	Right Ventricle	heart
5	chrX:154446400-154467800	Weak transcription	Pancreas	Pancrea
6	chrX:154446400-154471400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chrX:154446400-154472000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chrX:154447200-154471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chrX:154450800-154470200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chrX:154452800-154468400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chrX:154453200-154467800	Strong transcription	Dnd41	blood
12	chrX:154453200-154469200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chrX:154454400-154468600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chrX:154455000-154468200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chrX:154455600-154468400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chrX:154456800-154470000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chrX:154457600-154469600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chrX:154457600-154469800	Weak transcription	NHDF-Ad	bronchial
19	chrX:154457600-154471800	Weak transcription	NH-A	brain
20	chrX:154459400-154467800	Weak transcription	Fetal Brain Male	brain
21	chrX:154459400-154467800	Weak transcription	Psoas Muscle	Psoas
22	chrX:154461000-154467800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chrX:154461000-154468600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chrX:154462800-154468200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chrX:154462800-154468600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chrX:154463400-154471400	Weak transcription	Fetal Kidney	kidney
27	chrX:154463800-154468400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chrX:154464000-154468400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chrX:154464000-154469200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chrX:154464200-154467800	Strong transcription	Primary B cells from peripheral blood	blood
31	chrX:154464200-154467800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chrX:154464400-154467800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chrX:154464400-154468200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
34	chrX:154464600-154467800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chrX:154464600-154468200	Strong transcription	Liver	Liver
36	chrX:154464600-154468600	Strong transcription	Fetal Thymus	thymus
37	chrX:154464800-154467800	Strong transcription	Placenta	Placenta
38	chrX:154464800-154468600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chrX:154465600-154468400	Strong transcription	K562	blood
40	chrX:154465600-154490800	Weak transcription	Primary T cells from cord blood	blood
41	chrX:154466200-154467800	Weak transcription	Brain Cingulate Gyrus	brain
42	chrX:154466200-154468600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chrX:154466200-154469600	Weak transcription	Brain Angular Gyrus	brain
44	chrX:154466200-154470000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chrX:154466200-154470600	Weak transcription	Hela-S3	cervix
46	chrX:154466400-154468000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chrX:154466400-154468000	Weak transcription	Brain Germinal Matrix	brain
48	chrX:154466400-154468000	Weak transcription	NHLF	lung
49	chrX:154466400-154469000	Weak transcription	Colon Smooth Muscle	Colon
50	chrX:154466400-154469000	Weak transcription	HSMMtube	muscle

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