Variant report

Variant	rs2026132
Chromosome Location	chr9:100415840-100415841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100411427..100413125-chr9:100414736..100416807,2	K562	blood:
2	chr9:100399646..100402826-chr9:100413871..100416046,3	MCF-7	breast:
3	chr9:100399300..100401975-chr9:100415730..100418354,2	MCF-7	breast:
4	chr9:100410274..100416448-chr9:100436904..100442072,6	K562	blood:

Variant related genes	Relation type
ENSG00000136936	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10983030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10983447	0.84[EUR][1000 genomes]
rs1800975	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2036959	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2149986	0.81[ASN][1000 genomes]
rs2668792	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2668793	0.80[EUR][1000 genomes]
rs2668798	0.84[EUR][1000 genomes]
rs2773347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2773351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2773355	0.80[ASN][1000 genomes]
rs2805767	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];1.00[EUR][1000 genomes]
rs2805775	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805777	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs2805779	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805791	0.88[ASN][1000 genomes]
rs2805801	0.81[ASN][1000 genomes]
rs2805803	0.86[ASN][1000 genomes]
rs2805806	0.81[ASN][1000 genomes]
rs2805824	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2805825	0.81[EUR][1000 genomes]
rs2805826	0.80[EUR][1000 genomes]
rs2805828	1.00[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2805829	0.87[EUR][1000 genomes]
rs2805832	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2805837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2805839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2808668	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2808673	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2808675	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2808677	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2808685	0.80[EUR][1000 genomes]
rs2808686	0.92[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs2808689	0.81[EUR][1000 genomes]
rs2808691	0.81[EUR][1000 genomes]
rs2808703	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6478325	0.99[EUR][1000 genomes]
rs7853179	0.95[JPT][hapmap]
rs913912	0.88[ASN][1000 genomes]
rs958346	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[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	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2026132	XPA	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100398000-100418600	Weak transcription	Pancreas	Pancrea
2	chr9:100399200-100421400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:100399600-100426800	Weak transcription	Stomach Mucosa	stomach
4	chr9:100400800-100451600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:100401200-100429000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:100401200-100456000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:100402400-100422400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr9:100402400-100425000	Strong transcription	Primary B cells from cord blood	blood
9	chr9:100402400-100439600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:100402400-100451400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:100402400-100455600	Strong transcription	Dnd41	blood
12	chr9:100402600-100456000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr9:100402600-100456200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr9:100402800-100429000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:100402800-100454200	Strong transcription	Fetal Thymus	thymus
16	chr9:100402800-100456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:100403000-100422600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr9:100403000-100428400	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr9:100403000-100439400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:100403000-100439800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr9:100403000-100449400	Strong transcription	HSMM	muscle
22	chr9:100403000-100450400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr9:100403000-100454400	Strong transcription	Placenta	Placenta
24	chr9:100403000-100454600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:100403200-100454400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr9:100403200-100455000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr9:100403400-100434400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:100403400-100439600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:100403400-100444200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:100403600-100453800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr9:100403800-100436200	Strong transcription	Adipose Nuclei	Adipose
32	chr9:100403800-100439000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:100404000-100435800	Strong transcription	A549	lung
34	chr9:100404000-100449200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:100404400-100422200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr9:100404800-100455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:100405000-100437800	Strong transcription	GM12878-XiMat	blood
38	chr9:100405800-100438600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:100406200-100424400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:100406800-100416800	Weak transcription	NHLF	lung
41	chr9:100406800-100418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr9:100409400-100439800	Strong transcription	HMEC	breast
43	chr9:100409600-100433200	Strong transcription	Fetal Intestine Large	intestine
44	chr9:100409600-100440000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr9:100409800-100427800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:100410200-100437800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr9:100410200-100454000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr9:100410600-100421600	Weak transcription	Aorta	Aorta
49	chr9:100410600-100426200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:100410600-100426400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links