Variant report

Variant	rs5965106
Chromosome Location	chrX:65390966-65390967
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:64794740..64796696-chrX:65390516..65393019,2	K562	blood:
2	chrX:65380851..65384981-chrX:65390840..65394687,4	K562	blood:

Variant related genes	Relation type
ENSG00000089472	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1011526	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1028348	0.93[MEX][hapmap]
rs1068536	0.86[CEU][hapmap]
rs1068537	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap]
rs1068538	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap]
rs1090752	0.86[CEU][hapmap]
rs1090842	0.86[CEU][hapmap]
rs1091486	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs12395548	0.83[GIH][hapmap]
rs1264212	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1264216	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1264218	1.00[CEU][hapmap]
rs1325561	0.86[MEX][hapmap]
rs13440529	0.92[CEU][hapmap]
rs1415297	0.83[GIH][hapmap]
rs1456803	0.86[CEU][hapmap]
rs1456804	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap]
rs1456806	0.86[CEU][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap]
rs17301659	1.00[CEU][hapmap]
rs1989028	1.00[CEU][hapmap]
rs2054179	0.86[CEU][hapmap]
rs2198868	0.86[CEU][hapmap]
rs2198869	0.86[CEU][hapmap]
rs2206203	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4827365	0.86[CEU][hapmap]
rs4827449	0.86[MEX][hapmap]
rs585069	0.86[MEX][hapmap]
rs586789	0.86[MEX][hapmap]
rs587657	0.86[MEX][hapmap]
rs5918587	0.86[MEX][hapmap]
rs5918594	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap]
rs5918974	0.86[MEX][hapmap]
rs5919024	0.85[CEU][hapmap]
rs5919069	0.83[GIH][hapmap]
rs5964495	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs5964499	1.00[CEU][hapmap]
rs5964500	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs5965105	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs5965110	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs606886	0.86[MEX][hapmap]
rs651494	0.86[CEU][hapmap]
rs6624844	0.86[MEX][hapmap]
rs6624875	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs6624876	1.00[CEU][hapmap]
rs670546	0.86[MEX][hapmap]
rs699863	0.85[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap]
rs7054364	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs7062799	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs707298	0.86[CEU][hapmap]
rs707302	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap]
rs708966	0.86[CEU][hapmap];1.00[MEX][hapmap]
rs708968	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs708969	0.86[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap]
rs760866	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs760867	0.86[MEX][hapmap]
rs7891437	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs806538	0.86[CEU][hapmap]
rs806607	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs806608	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs806609	1.00[CEU][hapmap]
rs806610	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap]
rs809363	0.93[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.87[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	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
2	nsv995042	chrX:65121634-65953299	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active 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	40 gene(s)	inside rSNPs	diseases
3	nsv916393	chrX:65269672-65521616	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3350331	chrX:65287003-65495627	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:65383600-65442200	Weak transcription	Small Intestine	intestine
2	chrX:65384600-65435600	Weak transcription	Left Ventricle	heart
3	chrX:65384800-65392200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chrX:65384800-65395400	Weak transcription	Brain Hippocampus Middle	brain
5	chrX:65385400-65392200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chrX:65385400-65399000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chrX:65385600-65392400	Weak transcription	Ovary	ovary
8	chrX:65385600-65393000	Weak transcription	Fetal Lung	lung
9	chrX:65385600-65395000	Weak transcription	Brain Anterior Caudate	brain
10	chrX:65385600-65435600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chrX:65385800-65392600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chrX:65386000-65392200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chrX:65386000-65392400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chrX:65386000-65392400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chrX:65386000-65392600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chrX:65386000-65392600	Weak transcription	Stomach Smooth Muscle	stomach
17	chrX:65386000-65393400	Weak transcription	Fetal Stomach	stomach
18	chrX:65387200-65393200	Weak transcription	Fetal Kidney	kidney
19	chrX:65387400-65395400	Weak transcription	Rectal Smooth Muscle	rectum
20	chrX:65387600-65435400	Weak transcription	Aorta	Aorta
21	chrX:65388000-65391800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chrX:65388000-65392400	Strong transcription	K562	blood
23	chrX:65388000-65393200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chrX:65388000-65393400	Weak transcription	Fetal Intestine Small	intestine
25	chrX:65388200-65393400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chrX:65388200-65394800	Weak transcription	Colon Smooth Muscle	Colon
27	chrX:65388200-65417200	Weak transcription	Colonic Mucosa	Colon
28	chrX:65388400-65391600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chrX:65389400-65391200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chrX:65389600-65399600	Weak transcription	Fetal Heart	heart
31	chrX:65390400-65395800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chrX:65390600-65392000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chrX:65390600-65393200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chrX:65390800-65391000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chrX:65390800-65391600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chrX:65390800-65391800	Weak transcription	Duodenum Mucosa	Duodenum
37	chrX:65390800-65393400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chrX:65390800-65394200	Strong transcription	Fetal Intestine Large	intestine
39	chrX:65390800-65395000	Strong transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links