Variant report

Variant	rs2147072
Chromosome Location	chr9:110060155-110060156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110049612..110053509-chr9:110059334..110062914,3	K562	blood:
2	chr9:110054445..110058128-chr9:110059472..110062917,7	K562	blood:
3	chr9:110005542..110008121-chr9:110058915..110061761,2	MCF-7	breast:
4	chr9:110043397..110048376-chr9:110058875..110065071,10	K562	blood:
5	chr9:110044258..110048385-chr9:110059208..110064151,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119318	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10113916	0.84[CHB][hapmap]
rs10119641	0.84[CHB][hapmap]
rs10481632	0.84[CHB][hapmap]
rs10521083	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10732368	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739232	0.87[CHB][hapmap]
rs10739234	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10739236	0.85[CHD][hapmap]
rs10739237	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739238	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10759219	0.83[CHB][hapmap]
rs10759222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759223	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759225	0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs10759226	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759227	0.84[ASN][1000 genomes]
rs10816475	0.95[CHB][hapmap]
rs10816477	0.84[CHB][hapmap]
rs10816485	0.84[CHB][hapmap]
rs10816486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10816487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10816492	0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs10816493	0.91[ASN][1000 genomes]
rs10978767	0.89[CHB][hapmap]
rs10978769	0.83[CHB][hapmap]
rs10978770	0.83[CHB][hapmap]
rs10978775	0.84[CHB][hapmap]
rs10978791	0.84[CHB][hapmap]
rs10978798	0.90[ASN][1000 genomes]
rs11573709	0.84[LWK][hapmap];0.83[YRI][hapmap]
rs12345455	0.84[CHB][hapmap]
rs1323806	0.90[CHB][hapmap]
rs1323808	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1323809	0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs1408135	0.95[CHB][hapmap]
rs1535765	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1535766	0.83[CHB][hapmap]
rs1805329	0.84[CHB][hapmap]
rs1805332	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1805334	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1805335	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1886134	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1969798	0.93[ASN][1000 genomes]
rs1980725	0.94[ASN][1000 genomes]
rs2147071	0.94[ASN][1000 genomes]
rs2417783	0.87[ASN][1000 genomes]
rs2417784	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs2417785	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818367	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4278207	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4625087	0.92[ASN][1000 genomes]
rs4978404	0.81[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4978406	0.91[ASN][1000 genomes]
rs4978764	0.95[CHB][hapmap]
rs4978844	0.91[ASN][1000 genomes]
rs4978849	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs698475	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs7019341	0.89[ASN][1000 genomes]
rs7025563	0.87[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs7029997	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7030169	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7030555	0.94[ASN][1000 genomes]
rs7030631	0.94[ASN][1000 genomes]
rs7031906	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7035611	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7035725	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7038737	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7039041	0.94[ASN][1000 genomes]
rs7041137	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs7041497	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7043962	0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7046950	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7852295	0.83[CHB][hapmap]
rs7856112	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7856227	0.91[ASN][1000 genomes]
rs7859769	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7866312	0.83[CHB][hapmap]
rs7866353	0.83[CHB][hapmap]
rs7866797	0.83[CHB][hapmap]
rs7867544	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs817836	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs817840	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs817841	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs942291	0.84[CHB][hapmap]
rs942292	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs942293	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs9969728	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv831682	chr9:109937181-110075453	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv508560	chr9:110006490-110060539	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv519266	chr9:110049477-110085255	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2147072	RAD23B	cis	multi-tissue	Pritchard
rs2147072	RAD23B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110047600-110067200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:110048800-110061000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr9:110048800-110067800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:110048800-110069600	Weak transcription	Fetal Brain Male	brain
5	chr9:110049000-110061200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:110049000-110061400	Weak transcription	NH-A	brain
7	chr9:110049000-110063000	Enhancers	Liver	Liver
8	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:110049000-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:110049200-110067000	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:110049400-110067800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:110050200-110063200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:110051200-110066000	Weak transcription	Fetal Intestine Large	intestine
14	chr9:110051200-110067000	Weak transcription	Thymus	Thymus
15	chr9:110051600-110079200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:110052000-110066800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:110052200-110061200	Weak transcription	Dnd41	blood
18	chr9:110052600-110063200	Weak transcription	Placenta	Placenta
19	chr9:110052600-110067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:110052600-110067000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:110052600-110068600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:110052600-110068600	Weak transcription	Brain Germinal Matrix	brain
23	chr9:110052600-110068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:110052600-110069200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:110052800-110061200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:110052800-110066000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:110053400-110068600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:110053600-110061200	Weak transcription	Hela-S3	cervix
29	chr9:110053600-110063200	Weak transcription	Fetal Thymus	thymus
30	chr9:110053600-110063400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:110055600-110061200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr9:110055600-110063000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr9:110055600-110067600	Weak transcription	HSMMtube	muscle
34	chr9:110055600-110068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:110055800-110061200	Weak transcription	HMEC	breast
36	chr9:110055800-110068600	Weak transcription	Fetal Brain Female	brain
37	chr9:110055800-110068600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr9:110056000-110061200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr9:110056000-110062600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr9:110056400-110061200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:110056400-110061200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:110056400-110061600	Weak transcription	HSMM	muscle
43	chr9:110056400-110063400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr9:110056800-110061200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:110056800-110061600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:110056800-110062400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:110056800-110065800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr9:110056800-110068600	Weak transcription	Lung	lung
49	chr9:110057000-110060200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:110057000-110060200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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