Variant report

Variant	rs10882947
Chromosome Location	chr10:99266278-99266279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99255192..99260643-chr10:99260836..99267100,8	K562	blood:
2	chr10:99264711..99267352-chr10:99330266..99332362,2	MCF-7	breast:
3	chr10:99259143..99261299-chr10:99264874..99266683,2	K562	blood:
4	chr10:99265449..99267822-chr10:99277534..99279101,2	K562	blood:
5	chr10:99266125..99268587-chr10:99272459..99275467,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165887	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10786352	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882950	0.81[CHD][hapmap]
rs10882951	0.81[CHD][hapmap]
rs10882952	0.87[EUR][1000 genomes]
rs10882953	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs10882954	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11189247	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11189255	0.81[EUR][1000 genomes]
rs11591644	0.90[AMR][1000 genomes]
rs11592144	0.95[CEU][hapmap];0.89[CHD][hapmap]
rs11592973	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11593116	0.90[AMR][1000 genomes]
rs11595151	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11598766	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11812581	0.89[ASN][1000 genomes]
rs12767191	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29001259	0.90[AMR][1000 genomes]
rs29001262	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs29001311	1.00[JPT][hapmap]
rs29001315	0.90[AMR][1000 genomes]
rs34041345	0.89[ASN][1000 genomes]
rs34312169	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34452362	0.90[AMR][1000 genomes]
rs34759540	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6584123	1.00[CHB][hapmap]
rs7073097	0.90[AMR][1000 genomes]
rs7077917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090595	0.89[ASN][1000 genomes]
rs7090757	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7901283	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872106	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10882947	ABCC2	cis	parietal	SCAN
rs10882947	LOXL4	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99260200-99276800	Weak transcription	Pancreas	Pancrea
2	chr10:99260400-99269400	Weak transcription	Ovary	ovary
3	chr10:99260400-99271400	Weak transcription	Colon Smooth Muscle	Colon
4	chr10:99260400-99272000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:99260600-99267600	Weak transcription	Brain Anterior Caudate	brain
6	chr10:99260600-99267800	Weak transcription	Osteobl	bone
7	chr10:99260600-99268000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:99260600-99268000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:99260600-99268000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr10:99260600-99268200	Weak transcription	NH-A	brain
11	chr10:99260600-99270800	Weak transcription	Brain Angular Gyrus	brain
12	chr10:99260600-99271200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:99260800-99267600	Weak transcription	Brain Substantia Nigra	brain
14	chr10:99260800-99267800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr10:99260800-99267800	Weak transcription	HMEC	breast
16	chr10:99260800-99268000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:99260800-99268000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:99260800-99268000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:99260800-99270400	Weak transcription	Adipose Nuclei	Adipose
20	chr10:99260800-99276800	Weak transcription	HSMM	muscle
21	chr10:99261000-99266600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr10:99261000-99267800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr10:99261000-99267800	Weak transcription	NHLF	lung
24	chr10:99261000-99270800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:99261600-99267600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr10:99262000-99271600	Weak transcription	HepG2	liver
27	chr10:99262400-99267800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr10:99263400-99267600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr10:99263400-99271600	Weak transcription	Lung	lung
30	chr10:99263600-99270800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:99263600-99277800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr10:99263800-99277200	Weak transcription	HSMMtube	muscle
33	chr10:99263800-99277600	Weak transcription	Aorta	Aorta
34	chr10:99264000-99271200	Weak transcription	Right Atrium	heart
35	chr10:99264000-99271600	Weak transcription	Fetal Muscle Leg	muscle
36	chr10:99264000-99271600	Weak transcription	Right Ventricle	heart
37	chr10:99264200-99267800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:99264200-99268000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:99264200-99271200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr10:99264600-99267600	Weak transcription	Brain Hippocampus Middle	brain
41	chr10:99265000-99267600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:99265200-99267600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr10:99265600-99267600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:99266000-99266400	Enhancers	Fetal Lung	lung
45	chr10:99266200-99267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr10:99266200-99267600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr10:99266200-99267600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr10:99266200-99267800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr10:99266200-99270800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr10:99266200-99271200	Weak transcription	Left Ventricle	heart

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