Variant report

Variant	rs2805839
Chromosome Location	chr9:100422027-100422028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100395226..100397532-chr9:100421562..100424396,3	K562	blood:
2	chr9:100394763..100397690-chr9:100420038..100423613,3	MCF-7	breast:
3	chr9:100410166..100412202-chr9:100420931..100422531,3	K562	blood:
4	chr9:100421669..100424121-chr9:100433002..100435566,2	MCF-7	breast:
5	chr9:100422000..100424478-chr9:100450904..100452721,2	K562	blood:
6	chr9:100418467..100422475-chr9:100423692..100426910,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136925	Chromatin interaction
ENSG00000136937	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10983030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10983447	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1800975	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2026132	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]
rs2036959	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2668792	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2668793	0.81[EUR][1000 genomes]
rs2668798	0.83[AMR][1000 genomes];0.85[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];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2773351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2805767	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs2805775	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2805777	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.84[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2805824	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2805825	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2805826	0.81[EUR][1000 genomes]
rs2805828	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2805829	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2805832	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2805840	0.81[EUR][1000 genomes]
rs2808668	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2808673	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2808675	1.00[CEU][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2808677	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2808685	0.81[EUR][1000 genomes]
rs2808686	0.92[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2808687	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2808689	0.82[EUR][1000 genomes]
rs2808691	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2808692	0.81[EUR][1000 genomes]
rs2808701	0.81[EUR][1000 genomes]
rs2808703	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6478325	0.86[EUR][1000 genomes]
rs7853179	0.95[JPT][hapmap]
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];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[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
rs2805839	XPA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100399600-100426800	Weak transcription	Stomach Mucosa	stomach
2	chr9:100400800-100451600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:100401200-100429000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:100401200-100456000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr9:100402400-100422400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr9:100402400-100425000	Strong transcription	Primary B cells from cord blood	blood
7	chr9:100402400-100439600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:100402400-100451400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:100402400-100455600	Strong transcription	Dnd41	blood
10	chr9:100402600-100456000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:100402600-100456200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr9:100402800-100429000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:100402800-100454200	Strong transcription	Fetal Thymus	thymus
14	chr9:100402800-100456000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:100403000-100422600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr9:100403000-100428400	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr9:100403000-100439400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:100403000-100439800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:100403000-100449400	Strong transcription	HSMM	muscle
20	chr9:100403000-100450400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr9:100403000-100454400	Strong transcription	Placenta	Placenta
22	chr9:100403000-100454600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:100403200-100454400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr9:100403200-100455000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr9:100403400-100434400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:100403400-100439600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:100403400-100444200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:100403600-100453800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr9:100403800-100436200	Strong transcription	Adipose Nuclei	Adipose
30	chr9:100403800-100439000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:100404000-100435800	Strong transcription	A549	lung
32	chr9:100404000-100449200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:100404400-100422200	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:100404800-100455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:100405000-100437800	Strong transcription	GM12878-XiMat	blood
36	chr9:100405800-100438600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:100406200-100424400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:100409400-100439800	Strong transcription	HMEC	breast
39	chr9:100409600-100433200	Strong transcription	Fetal Intestine Large	intestine
40	chr9:100409600-100440000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:100409800-100427800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:100410200-100437800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr9:100410200-100454000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr9:100410600-100426200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr9:100410600-100426400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr9:100411200-100423000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:100411200-100451000	Strong transcription	Liver	Liver
48	chr9:100411400-100426200	Weak transcription	Esophagus	oesophagus
49	chr9:100412400-100423200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:100412400-100423200	Strong transcription	Fetal Lung	lung

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