Variant report

Variant	rs10887876
Chromosome Location	chr10:90745130-90745131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:90740958..90743337-chr10:90743863..90746089,2	MCF-7	breast:
2	chr10:90693883..90696142-chr10:90743433..90746344,2	MCF-7	breast:
3	chr10:90732274..90733956-chr10:90744737..90747226,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10788624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202917	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11202922	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1468063	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap]
rs1800682	0.81[ASN][1000 genomes]
rs1926195	0.80[CHB][hapmap]
rs1926197	0.81[ASN][1000 genomes]
rs1926199	0.81[ASN][1000 genomes]
rs1926200	0.81[ASN][1000 genomes]
rs1926201	0.81[ASN][1000 genomes]
rs2234767	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3758485	0.81[ASN][1000 genomes]
rs3781204	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4934433	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4934434	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs6586160	0.80[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs6586161	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7076197	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7097467	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7914490	0.81[ASN][1000 genomes]
rs9325603	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9658685	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9658767	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs9658769	1.00[CEU][hapmap];0.95[JPT][hapmap]

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	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10887876	SLC16A12	cis	parietal	SCAN
rs10887876	FAS	cis	cerebellum	SCAN
rs10887876	FAS	cis	parietal	SCAN
rs10887876	ANKRD1	cis	cerebellum	SCAN
rs10887876	ACTA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90735200-90749800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr10:90735600-90746400	Weak transcription	HepG2	liver
3	chr10:90735600-90748600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr10:90735600-90749200	Weak transcription	Fetal Muscle Leg	muscle
5	chr10:90735600-90749200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr10:90735800-90746400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:90738200-90747800	Enhancers	Colon Smooth Muscle	Colon
8	chr10:90739200-90745200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:90739400-90749400	Weak transcription	NHEK	skin
10	chr10:90739600-90746400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:90739600-90747200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:90739600-90748600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:90739600-90749000	Weak transcription	Adipose Nuclei	Adipose
14	chr10:90739600-90749200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:90739800-90749200	Weak transcription	HMEC	breast
16	chr10:90740200-90749200	Weak transcription	Left Ventricle	heart
17	chr10:90740400-90746400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:90740600-90745200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:90740800-90749200	Weak transcription	NH-A	brain
20	chr10:90741000-90745200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:90741000-90747200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:90741000-90747400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:90741000-90749200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:90741000-90749400	Weak transcription	Spleen	Spleen
25	chr10:90741600-90745600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr10:90741600-90749200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:90741600-90749200	Weak transcription	Psoas Muscle	Psoas
28	chr10:90741600-90749400	Weak transcription	HSMM	muscle
29	chr10:90742600-90745400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:90742600-90746400	Weak transcription	Fetal Kidney	kidney
31	chr10:90742800-90746000	Weak transcription	NHLF	lung
32	chr10:90742800-90747200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:90742800-90749800	Weak transcription	Brain Hippocampus Middle	brain
34	chr10:90743000-90746600	Weak transcription	Liver	Liver
35	chr10:90743200-90746200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:90743200-90746400	Weak transcription	NHDF-Ad	bronchial
37	chr10:90743200-90746600	Enhancers	Stomach Smooth Muscle	stomach
38	chr10:90743600-90745400	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr10:90743600-90746600	Enhancers	Ovary	ovary
40	chr10:90743800-90746000	Enhancers	Aorta	Aorta
41	chr10:90743800-90746800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr10:90743800-90749600	Weak transcription	Fetal Intestine Large	intestine
43	chr10:90744200-90745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:90744200-90745600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr10:90744200-90746000	Weak transcription	Fetal Lung	lung
46	chr10:90744200-90746400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr10:90744200-90746400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:90744200-90749200	Weak transcription	Fetal Stomach	stomach
49	chr10:90744200-90749200	Weak transcription	Right Atrium	heart
50	chr10:90744200-90749600	Weak transcription	Fetal Intestine Small	intestine

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