Variant report

Variant	rs10115088
Chromosome Location	chr9:3553220-3553221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:3525276..3528835-chr9:3550312..3553515,4	K562	blood:
2	chr9:3525472..3528228-chr9:3550312..3553459,3	K562	blood:
3	chr9:3524890..3527921-chr9:3551840..3557336,6	MCF-7	breast:
4	chr9:3525759..3527447-chr9:3552151..3553813,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNV2-13	chr9:3552597-3553312	NONHSAT130027

Variant related genes	Relation type
ENSG00000232104	Chromatin interaction
ENSG00000080298	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10114162	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10114838	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10115578	0.87[CEU][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs10118702	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119982	0.87[CEU][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]
rs10121096	0.85[CEU][hapmap]
rs10758299	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10814189	0.86[JPT][hapmap]
rs10814190	0.86[JPT][hapmap]
rs10814208	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10814219	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10814233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10814235	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10814250	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10814251	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10972435	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10972438	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133463	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1133467	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12004862	0.87[CEU][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs12238307	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs12340274	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs12353393	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs12684702	0.89[ASN][1000 genomes]
rs1342542	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs2027089	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28510559	0.80[EUR][1000 genomes]
rs3954945	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7022948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026025	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7027862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7041399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7042747	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7045092	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7847562	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7857554	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7858486	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7861625	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs7864107	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867083	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7871094	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871777	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7873538	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs881167	0.85[ASW][hapmap];0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs9774864	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9792451	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv1022795	chr9:3436845-3744623	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10115088	RP11-509J21.1	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3527400-3567600	Weak transcription	Ovary	ovary
2	chr9:3528600-3554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:3528800-3553600	Weak transcription	Adipose Nuclei	Adipose
4	chr9:3528800-3560600	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:3529000-3579000	Weak transcription	HSMMtube	muscle
6	chr9:3530000-3556400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:3530200-3553600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr9:3531000-3575800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:3531200-3564600	Weak transcription	HSMM	muscle
10	chr9:3531800-3579000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:3541800-3553400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:3542600-3556800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:3544000-3555800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr9:3544400-3554000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:3546600-3563600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:3546800-3554200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:3546800-3556000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr9:3547600-3572800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:3547800-3562800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:3548200-3560200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:3548400-3554000	Weak transcription	Left Ventricle	heart
22	chr9:3549000-3558400	Weak transcription	Aorta	Aorta
23	chr9:3549400-3553400	Weak transcription	Brain Anterior Caudate	brain
24	chr9:3549400-3570200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr9:3549800-3553600	Weak transcription	Primary T cells from cord blood	blood
26	chr9:3549800-3562600	Weak transcription	Lung	lung
27	chr9:3549800-3572800	Weak transcription	Right Ventricle	heart
28	chr9:3550000-3566000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:3550000-3593000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:3551000-3556800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:3551000-3571200	Weak transcription	Thymus	Thymus
32	chr9:3551200-3553400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:3551200-3556400	Weak transcription	K562	blood
34	chr9:3551400-3563000	Weak transcription	Primary B cells from cord blood	blood
35	chr9:3552000-3557400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr9:3552200-3555600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:3552400-3563000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr9:3552600-3555200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:3552600-3563200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr9:3552800-3554400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:3552800-3555000	Weak transcription	Liver	Liver
42	chr9:3553200-3553600	Enhancers	Brain Angular Gyrus	brain
43	chr9:3553200-3553600	Enhancers	Brain Hippocampus Middle	brain
44	chr9:3553200-3553600	Enhancers	NHEK	skin
45	chr9:3553200-3554200	Enhancers	Brain Substantia Nigra	brain
46	chr9:3553200-3554600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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