Variant report

Variant	rs9870952
Chromosome Location	chr3:88100480-88100481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88089281..88093496-chr3:88099183..88102618,6	MCF-7	breast:
2	chr3:88080562..88082885-chr3:88098755..88100923,2	MCF-7	breast:
3	chr3:88095316..88097953-chr3:88099604..88102152,4	MCF-7	breast:
4	chr1:4807916..4809436-chr3:88099508..88101022,2	MCF-7	breast:
5	chr3:88090384..88092105-chr3:88098144..88100767,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1006895	0.97[AFR][1000 genomes]
rs1040319	0.97[AFR][1000 genomes]
rs1051413	0.97[AFR][1000 genomes]
rs1063597	0.97[AFR][1000 genomes]
rs1063603	0.97[AFR][1000 genomes]
rs10865625	0.92[AFR][1000 genomes]
rs12632529	0.95[AFR][1000 genomes]
rs13058811	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13060730	0.93[AFR][1000 genomes]
rs13076170	0.93[AFR][1000 genomes]
rs13098157	0.95[AFR][1000 genomes]
rs13100870	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1991659	0.91[AFR][1000 genomes]
rs2049817	0.94[AFR][1000 genomes]
rs2116149	0.97[AFR][1000 genomes]
rs3732776	0.97[AFR][1000 genomes]
rs4273396	0.82[AFR][1000 genomes]
rs4368523	0.92[AFR][1000 genomes]
rs4378991	0.85[AFR][1000 genomes]
rs4416403	0.86[AFR][1000 genomes]
rs4438681	0.86[AFR][1000 genomes]
rs4502603	0.92[AFR][1000 genomes]
rs4588391	0.92[AFR][1000 genomes]
rs4611846	0.93[AFR][1000 genomes]
rs4638995	0.90[AFR][1000 genomes]
rs4858982	0.95[AFR][1000 genomes]
rs4858983	0.95[AFR][1000 genomes]
rs4858985	0.92[AFR][1000 genomes]
rs4858992	0.90[AFR][1000 genomes]
rs4858994	0.89[AFR][1000 genomes]
rs6551268	0.86[AFR][1000 genomes]
rs6777019	0.94[AFR][1000 genomes]
rs6790426	0.81[AFR][1000 genomes]
rs6790629	0.84[AFR][1000 genomes]
rs6799233	0.86[AFR][1000 genomes]
rs7618472	0.86[AFR][1000 genomes]
rs7633121	0.87[AFR][1000 genomes]
rs7648096	0.86[AFR][1000 genomes]
rs9310066	0.94[AFR][1000 genomes]
rs9310067	0.90[AFR][1000 genomes]
rs9310068	0.89[AFR][1000 genomes]
rs959048	0.95[AFR][1000 genomes]
rs959049	0.95[AFR][1000 genomes]
rs959050	0.93[AFR][1000 genomes]
rs9821517	0.92[AFR][1000 genomes]
rs9829873	0.86[AFR][1000 genomes]
rs9835771	0.86[AFR][1000 genomes]
rs9840953	0.97[AFR][1000 genomes]
rs9841189	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9845776	0.86[AFR][1000 genomes]
rs9847019	0.86[AFR][1000 genomes]
rs9850892	0.97[AFR][1000 genomes]
rs9851328	0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9864220	0.92[AFR][1000 genomes]
rs9865990	0.96[AFR][1000 genomes]
rs9866349	0.95[AFR][1000 genomes]
rs9872602	0.86[AFR][1000 genomes]
rs9879044	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9870952	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs9870952	C3orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88088400-88104200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:88089000-88102800	Weak transcription	NHDF-Ad	bronchial
3	chr3:88091200-88104600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:88093800-88103400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:88093800-88106400	Weak transcription	Right Atrium	heart
6	chr3:88094200-88103400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:88095000-88104600	Weak transcription	Spleen	Spleen
8	chr3:88095800-88100600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:88095800-88102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:88095800-88103000	Weak transcription	Dnd41	blood
11	chr3:88095800-88103400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:88095800-88103800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:88095800-88104000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:88095800-88104000	Weak transcription	Osteobl	bone
15	chr3:88095800-88104200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:88095800-88104200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:88095800-88104200	Weak transcription	HMEC	breast
18	chr3:88096000-88104600	Weak transcription	Aorta	Aorta
19	chr3:88096200-88101000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:88096200-88102600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:88097000-88104200	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:88097200-88101600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:88097400-88102600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:88097400-88104200	Weak transcription	HUVEC	blood vessel
25	chr3:88097800-88103800	Weak transcription	HSMM	muscle
26	chr3:88098800-88104400	Weak transcription	K562	blood
27	chr3:88099000-88107200	Weak transcription	Small Intestine	intestine
28	chr3:88099600-88102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:88099800-88104200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:88100000-88104600	Weak transcription	Brain Substantia Nigra	brain
31	chr3:88100200-88102200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:88100200-88103000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:88100200-88103800	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:88100200-88106800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:88100400-88100600	Enhancers	Left Ventricle	heart
36	chr3:88100400-88101400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:88100400-88102000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:88100400-88102200	Weak transcription	Monocytes-CD14+_RO01746	blood

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