Variant report

Variant	rs10512136
Chromosome Location	chr9:86252152-86252153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86247034..86248660-chr9:86250680..86252326,2	K562	blood:
2	chr9:86248664..86251363-chr9:86251483..86253533,2	MCF-7	breast:
3	chr9:86249957..86252559-chr9:86321303..86324119,2	MCF-7	breast:
4	chr9:86251432..86253303-chr9:86255236..86258131,2	MCF-7	breast:
5	chr9:86247178..86252278-chr9:86254565..86260519,7	MCF-7	breast:
6	chr9:86251932..86254568-chr9:86256964..86260409,3	K562	blood:

Variant related genes	Relation type
ENSG00000254473	Chromatin interaction
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10512137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1056073	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10746717	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10780616	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780617	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780618	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780619	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10780620	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10780622	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10780623	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10780624	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10780625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10868035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10868036	0.89[AMR][1000 genomes]
rs10868037	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10868038	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10868042	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10868043	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11140198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11140202	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11140209	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs11140212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11140221	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11140223	0.80[AMR][1000 genomes]
rs11791175	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1333861	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]
rs1333862	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1537502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537503	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1961941	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2282220	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2811921	0.86[CHB][hapmap]
rs3750409	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750410	0.95[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3814505	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4146740	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4454364	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs4877790	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4877791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4877793	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4877794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4877796	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes]
rs4877797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4877799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4877800	0.83[AMR][1000 genomes]
rs7046388	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72618136	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7860614	0.86[AMR][1000 genomes]
rs7863266	0.86[AMR][1000 genomes]
rs7866234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7871055	0.90[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs868917	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][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	nsv516587	chr9:86226119-86255765	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv973848	chr9:86241130-86260149	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10512136	RP11-522I20.3	cis	Whole Blood	GTEx
rs10512136	RP11-522I20.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86238600-86265000	Weak transcription	Ovary	ovary
2	chr9:86238800-86254600	Weak transcription	Left Ventricle	heart
3	chr9:86238800-86260600	Weak transcription	Right Ventricle	heart
4	chr9:86238800-86264600	Weak transcription	Psoas Muscle	Psoas
5	chr9:86239000-86264800	Weak transcription	HMEC	breast
6	chr9:86239000-86265200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:86239200-86261000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr9:86239400-86254400	Weak transcription	Brain Anterior Caudate	brain
9	chr9:86239400-86254400	Weak transcription	Brain Substantia Nigra	brain
10	chr9:86239400-86266200	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:86239400-86266400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:86239600-86260800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:86239600-86260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:86239600-86265000	Weak transcription	HUVEC	blood vessel
15	chr9:86239600-86266600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:86239600-86272200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:86239800-86266800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:86240200-86265000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr9:86240400-86254600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr9:86242200-86256600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:86242400-86253800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:86242400-86257000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:86242400-86264800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:86242600-86265000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr9:86243200-86260800	Weak transcription	Primary B cells from cord blood	blood
26	chr9:86243200-86261000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:86243200-86269600	Weak transcription	Pancreas	Pancrea
28	chr9:86243600-86264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr9:86243600-86266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr9:86244000-86260600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:86244000-86260800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr9:86244200-86264600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:86244400-86254200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:86244400-86262200	Weak transcription	A549	lung
35	chr9:86244400-86264600	Weak transcription	NHLF	lung
36	chr9:86244600-86257600	Weak transcription	Lung	lung
37	chr9:86244600-86257800	Weak transcription	Primary T cells from cord blood	blood
38	chr9:86244600-86258000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:86244600-86260000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:86244600-86260200	Weak transcription	NHEK	skin
41	chr9:86244800-86254400	Weak transcription	HSMM	muscle
42	chr9:86244800-86258200	Weak transcription	GM12878-XiMat	blood
43	chr9:86244800-86260400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:86244800-86260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:86244800-86261200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:86244800-86278800	Weak transcription	Spleen	Spleen
47	chr9:86244800-86285800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr9:86245000-86252200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:86245000-86257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:86245000-86257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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