Variant report

Variant	rs1333861
Chromosome Location	chr9:86318398-86318399
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86313399..86317163-chr9:86318289..86320003,3	K562	blood:
2	chr9:85806373..85808943-chr9:86317135..86320093,2	K562	blood:
3	chr9:86236927..86238886-chr9:86316132..86318961,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148057	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10512136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10512137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056073	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10746717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780616	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10780617	0.88[AMR][1000 genomes]
rs10780618	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes]
rs10780619	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs10780620	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10780622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780623	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10780624	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868036	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10868037	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10868038	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868042	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868043	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11140198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11140202	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140209	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11140212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11140221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140223	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11791175	1.00[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12235741	0.83[AMR][1000 genomes]
rs1333862	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1537503	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs17080575	0.83[AMR][1000 genomes]
rs1961941	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282220	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2811921	0.85[CHB][hapmap];0.87[YRI][hapmap]
rs3750409	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3750410	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs3814505	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3814507	0.83[AMR][1000 genomes]
rs4146740	0.81[EUR][1000 genomes]
rs4454364	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877790	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4877791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4877793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4877794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4877796	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877800	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7046388	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72618136	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7860614	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7863266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7866234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7871055	0.94[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs868917	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1333861	RP11-522I20.3	cis	Whole Blood	GTEx
rs1333861	RP11-522I20.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
2	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:86294200-86320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
5	chr9:86297000-86320000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:86297600-86319800	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:86298000-86320400	Weak transcription	Fetal Intestine Large	intestine
9	chr9:86298600-86320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:86298800-86320800	Weak transcription	Fetal Thymus	thymus
11	chr9:86299600-86319400	Weak transcription	Fetal Stomach	stomach
12	chr9:86299600-86320000	Weak transcription	Fetal Intestine Small	intestine
13	chr9:86300400-86320400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:86300600-86320400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:86301000-86320800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr9:86304400-86320800	Weak transcription	Brain Anterior Caudate	brain
17	chr9:86307600-86320400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:86310400-86320600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:86311200-86320800	Weak transcription	Fetal Lung	lung
20	chr9:86311600-86320000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr9:86311800-86321000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:86312000-86319400	Weak transcription	Primary B cells from cord blood	blood
23	chr9:86312800-86320800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr9:86313000-86319400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr9:86313200-86320800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr9:86313400-86319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:86313600-86321000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr9:86313800-86319400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr9:86314400-86319800	Enhancers	Primary T cells from cord blood	blood
30	chr9:86314400-86320800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr9:86314600-86319400	Weak transcription	Spleen	Spleen
32	chr9:86314600-86320200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr9:86314600-86321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:86314600-86321400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:86314600-86321400	Weak transcription	Gastric	stomach
36	chr9:86314600-86321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:86315000-86320000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:86315000-86320400	Weak transcription	Fetal Heart	heart
39	chr9:86315000-86320600	Weak transcription	Stomach Mucosa	stomach
40	chr9:86315200-86319800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:86315200-86321400	Weak transcription	Aorta	Aorta
42	chr9:86315600-86320400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:86315800-86319800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:86315800-86320800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr9:86315800-86320800	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:86316000-86320200	Weak transcription	Right Ventricle	heart
47	chr9:86316000-86320400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr9:86316000-86320600	Weak transcription	Brain Substantia Nigra	brain
49	chr9:86316000-86321400	Weak transcription	Pancreas	Pancrea
50	chr9:86316000-86321800	Weak transcription	Lung	lung

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