Variant report

Variant	rs1805335
Chromosome Location	chr9:110081018-110081019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:110070353..110073170-chr9:110078217..110082315,4	MCF-7	breast:
2	chr9:110079426..110081266-chr9:110101654..110103447,2	MCF-7	breast:
3	chr9:110065252..110067384-chr9:110080833..110082892,2	K562	blood:
4	chr9:110079143..110082107-chr9:110082961..110085070,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10521083	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10732368	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739232	0.81[CHB][hapmap]
rs10739234	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10739236	0.82[CHD][hapmap]
rs10739237	0.87[ASN][1000 genomes]
rs10739238	0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs10759222	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759223	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759225	0.89[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759227	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10816475	0.89[CHB][hapmap]
rs10816486	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816487	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816492	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10816493	0.94[ASN][1000 genomes]
rs10978767	0.84[CHB][hapmap]
rs10978769	0.89[CHB][hapmap]
rs10978798	0.93[ASN][1000 genomes]
rs11573709	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs1323806	0.84[CHB][hapmap]
rs1323808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323809	0.89[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1408135	0.89[CHB][hapmap]
rs1535765	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1805332	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1805334	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1886134	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1969798	0.90[ASN][1000 genomes]
rs1980725	0.91[ASN][1000 genomes]
rs2147071	0.91[ASN][1000 genomes]
rs2147072	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]
rs2417783	0.84[ASN][1000 genomes]
rs2417784	0.85[CHD][hapmap]
rs2417785	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818367	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4278207	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4625087	0.89[ASN][1000 genomes]
rs4978404	0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs4978406	0.94[ASN][1000 genomes]
rs4978764	0.89[CHB][hapmap]
rs4978844	0.94[ASN][1000 genomes]
rs4978849	0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs698475	0.85[CHD][hapmap]
rs7019341	0.92[ASN][1000 genomes]
rs7025563	0.80[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs7029997	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7030169	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7030555	0.91[ASN][1000 genomes]
rs7030631	0.91[ASN][1000 genomes]
rs7031906	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7035611	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7035725	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7038737	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7039041	0.91[ASN][1000 genomes]
rs7041137	0.82[CHD][hapmap]
rs7041497	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7043962	0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs7046950	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7856112	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856227	0.94[ASN][1000 genomes]
rs7859769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7867544	0.84[CHB][hapmap];0.85[CHD][hapmap]
rs817836	0.85[CHD][hapmap]
rs817840	0.82[CHD][hapmap]
rs817841	0.82[CHD][hapmap]
rs942292	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942293	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1805335	RAD23B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110058600-110098600	Weak transcription	Small Intestine	intestine
2	chr9:110061400-110094600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:110064000-110085000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:110065200-110089200	Strong transcription	Fetal Thymus	thymus
5	chr9:110065600-110098600	Strong transcription	Dnd41	blood
6	chr9:110070200-110104400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:110070400-110085000	Weak transcription	Colonic Mucosa	Colon
8	chr9:110070400-110099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:110071400-110084000	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:110071400-110103000	Weak transcription	Stomach Mucosa	stomach
11	chr9:110071800-110084400	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:110074200-110082600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:110074200-110083000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr9:110074200-110083200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:110074200-110088200	Strong transcription	Fetal Intestine Large	intestine
16	chr9:110075000-110084800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:110075000-110088000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:110075200-110084800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:110075200-110084800	Weak transcription	Spleen	Spleen
20	chr9:110075200-110090600	Weak transcription	Right Ventricle	heart
21	chr9:110075200-110093400	Weak transcription	Esophagus	oesophagus
22	chr9:110076000-110089400	Strong transcription	Primary hematopoietic stem cells	blood
23	chr9:110076200-110084600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:110076200-110087800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:110076400-110084000	Weak transcription	Hela-S3	cervix
26	chr9:110076400-110084600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:110076800-110084200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr9:110076800-110084600	Weak transcription	Brain Substantia Nigra	brain
29	chr9:110076800-110088200	Weak transcription	Fetal Brain Male	brain
30	chr9:110077000-110084400	Weak transcription	Fetal Brain Female	brain
31	chr9:110077200-110086200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:110077200-110090600	Weak transcription	Brain Germinal Matrix	brain
33	chr9:110077400-110084000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:110077400-110084200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:110077600-110093800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr9:110078000-110082400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:110078800-110084200	Weak transcription	Fetal Stomach	stomach
38	chr9:110078800-110084400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr9:110078800-110084600	Strong transcription	Liver	Liver
40	chr9:110078800-110087000	Weak transcription	Fetal Intestine Small	intestine
41	chr9:110079000-110082600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:110079000-110089800	Strong transcription	NH-A	brain
43	chr9:110079200-110081800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:110079200-110085400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr9:110079200-110087800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:110079200-110088200	Strong transcription	K562	blood
47	chr9:110079400-110081600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr9:110079400-110084600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr9:110079400-110084800	Weak transcription	Left Ventricle	heart
50	chr9:110079400-110088000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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