Variant report

Variant	rs5965004
Chromosome Location	chrX:64942719-64942720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chrX:64815276..64815912-chrX:64942286..64943257,2	K562	blood:
2	chrX:64887079..64888676-chrX:64940058..64942737,2	K562	blood:
3	chrX:64887014..64890188-chrX:64939207..64943512,5	K562	blood:

Variant related genes	Relation type
ENSG00000147065	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12397033	1.00[MEX][hapmap]
rs16989666	1.00[MEX][hapmap]
rs16989770	1.00[GIH][hapmap]
rs5964999	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs5965003	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs5965006	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs5965007	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs5965030	0.85[ASW][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs6524991	1.00[MEX][hapmap]
rs6525004	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap]
rs6525006	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs6525007	0.87[GIH][hapmap];1.00[MEX][hapmap]
rs6624812	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap]
rs6624823	1.00[MEX][hapmap]
rs7050592	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7051717	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7061281	1.00[ASW][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap]
rs7887261	1.00[GIH][hapmap]

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	esv3429625	chrX:64787230-65458721	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:64926400-64948600	Weak transcription	Fetal Lung	lung
2	chrX:64926600-64949400	Weak transcription	Esophagus	oesophagus
3	chrX:64926800-64949400	Weak transcription	Aorta	Aorta
4	chrX:64927000-64945000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chrX:64927000-64949200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chrX:64927200-64945000	Weak transcription	Osteobl	bone
7	chrX:64927200-64950400	Weak transcription	Gastric	stomach
8	chrX:64927600-64948200	Weak transcription	Fetal Muscle Leg	muscle
9	chrX:64927800-64945400	Weak transcription	Brain Cingulate Gyrus	brain
10	chrX:64927800-64945800	Weak transcription	Brain Substantia Nigra	brain
11	chrX:64927800-64945800	Weak transcription	HMEC	breast
12	chrX:64927800-64946800	Weak transcription	Brain Anterior Caudate	brain
13	chrX:64927800-64964200	Weak transcription	Fetal Heart	heart
14	chrX:64932000-64946600	Weak transcription	Psoas Muscle	Psoas
15	chrX:64932200-64947600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chrX:64932200-64947800	Weak transcription	Fetal Kidney	kidney
17	chrX:64932200-64949400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chrX:64932400-64948400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chrX:64933400-64950200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chrX:64934200-64946000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chrX:64936200-64946600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chrX:64936400-64946400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chrX:64936400-64947000	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chrX:64936400-64951600	Weak transcription	Fetal Intestine Large	intestine
25	chrX:64936400-64963400	Strong transcription	Dnd41	blood
26	chrX:64936600-64943600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chrX:64936800-64943400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chrX:64936800-64952600	Weak transcription	Rectal Smooth Muscle	rectum
29	chrX:64937400-64947800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chrX:64937600-64946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chrX:64937600-64947200	Weak transcription	Fetal Muscle Trunk	muscle
32	chrX:64937600-64947800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chrX:64937800-64943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chrX:64937800-64943200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chrX:64937800-64943200	Weak transcription	Stomach Smooth Muscle	stomach
36	chrX:64937800-64943600	Weak transcription	Left Ventricle	heart
37	chrX:64937800-64947600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chrX:64937800-64949400	Weak transcription	Ovary	ovary
39	chrX:64937800-64949400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chrX:64938000-64946200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chrX:64938000-64949400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chrX:64938200-64943200	Weak transcription	NH-A	brain
43	chrX:64938200-64943200	Weak transcription	NHEK	skin
44	chrX:64939200-64947800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chrX:64939400-64945600	Weak transcription	Brain Hippocampus Middle	brain
46	chrX:64939600-64943000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chrX:64939600-64947600	Genic enhancers	Primary B cells from peripheral blood	blood
48	chrX:64939800-64943200	Weak transcription	Fetal Thymus	thymus
49	chrX:64939800-64945400	Genic enhancers	Primary monocytes fromperipheralblood	blood
50	chrX:64940000-64945400	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links