Variant report

Variant	rs7913199
Chromosome Location	chr10:116294497-116294498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116285931..116289636-chr10:116291274..116296200,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099204	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11196778	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12413487	0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1333688	0.83[AMR][1000 genomes]
rs2483534	0.83[AMR][1000 genomes]
rs2483535	0.83[CHB][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2483536	0.83[AMR][1000 genomes]
rs2483537	0.83[AMR][1000 genomes]
rs2483538	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2483539	0.83[CHB][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2483540	0.83[AMR][1000 genomes]
rs2483541	0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2483542	0.83[AMR][1000 genomes]
rs2483543	0.81[AMR][1000 genomes]
rs2483544	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs2483545	0.83[AMR][1000 genomes]
rs2483546	0.83[AMR][1000 genomes]
rs2483548	0.86[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2483549	0.88[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2483550	0.83[AMR][1000 genomes]
rs2483552	0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs2483553	0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2483554	0.83[AMR][1000 genomes]
rs2483555	0.83[AMR][1000 genomes]
rs2483556	0.83[AMR][1000 genomes]
rs2483557	0.87[AMR][1000 genomes]
rs2483558	0.87[AMR][1000 genomes]
rs2483559	0.86[AMR][1000 genomes]
rs2483560	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2483563	0.80[AMR][1000 genomes]
rs2483568	0.86[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2483578	0.90[GIH][hapmap];0.84[TSI][hapmap]
rs2483583	0.86[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs2483590	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2497663	0.86[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2497725	0.83[CHB][hapmap];0.83[AMR][1000 genomes]
rs2497726	0.82[AMR][1000 genomes]
rs2497727	0.83[AMR][1000 genomes]
rs2497728	0.83[AMR][1000 genomes]
rs2497729	0.83[AMR][1000 genomes]
rs2497730	0.83[CHB][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2497731	0.83[CHB][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs2497732	0.83[AMR][1000 genomes]
rs2497733	0.88[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2497735	0.82[AMR][1000 genomes]
rs2497736	0.83[AMR][1000 genomes]
rs2497737	0.83[AMR][1000 genomes]
rs2497738	0.83[AMR][1000 genomes]
rs2497739	0.83[AMR][1000 genomes]
rs2497740	0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs2497741	0.86[AMR][1000 genomes]
rs2497742	0.86[AMR][1000 genomes]
rs2497743	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2497744	0.82[AMR][1000 genomes]
rs2497747	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2497748	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2497749	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4128920	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4998667	0.90[GIH][hapmap];0.90[TSI][hapmap]
rs58938015	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60588618	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085345	0.81[AMR][1000 genomes]
rs7091986	0.83[AMR][1000 genomes]
rs72826986	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72826987	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915116	0.83[AMR][1000 genomes]
rs7915452	0.82[AMR][1000 genomes]
rs9325544	0.88[AMR][1000 genomes]
rs9421186	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9421190	0.84[EUR][1000 genomes]
rs985273	0.86[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7913199	PDCD4	cis	cerebellum	SCAN
rs7913199	PPP1R16A	trans	cerebellum	SCAN
rs7913199	SHOC2	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116286800-116298000	Weak transcription	Esophagus	oesophagus
2	chr10:116287000-116296600	Weak transcription	HSMM	muscle
3	chr10:116287000-116298200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:116287000-116298200	Weak transcription	Lung	lung
5	chr10:116287000-116301200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:116287200-116299400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr10:116287200-116299400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:116287200-116300600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr10:116287200-116301600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:116287200-116307200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:116287400-116294800	Weak transcription	Fetal Kidney	kidney
12	chr10:116287400-116296200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:116287400-116297200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:116287400-116297400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:116287400-116297400	Weak transcription	Fetal Heart	heart
16	chr10:116287400-116297600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr10:116287400-116297800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr10:116287400-116298000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:116287400-116298000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr10:116287400-116298200	Weak transcription	HMEC	breast
21	chr10:116287400-116300400	Weak transcription	Brain Hippocampus Middle	brain
22	chr10:116287400-116300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:116287400-116300600	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:116287400-116300800	Weak transcription	Fetal Intestine Large	intestine
25	chr10:116287400-116303200	Weak transcription	Brain Anterior Caudate	brain
26	chr10:116287400-116303800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr10:116287400-116310600	Weak transcription	Brain Angular Gyrus	brain
28	chr10:116287400-116310600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr10:116287600-116296400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr10:116287600-116297200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr10:116287600-116298000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr10:116287600-116298000	Weak transcription	Fetal Muscle Leg	muscle
33	chr10:116288800-116298000	Weak transcription	Right Ventricle	heart
34	chr10:116289400-116295600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:116289400-116295600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:116289400-116295600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr10:116289400-116296400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr10:116289600-116296600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr10:116289600-116296600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr10:116291600-116294600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:116291600-116295800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr10:116291800-116296800	Strong transcription	Liver	Liver
43	chr10:116292000-116296800	Strong transcription	HSMMtube	muscle
44	chr10:116292400-116298000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr10:116292400-116303800	Weak transcription	Pancreas	Pancrea
46	chr10:116292600-116297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:116292600-116297800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr10:116292600-116298000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr10:116292800-116294600	Weak transcription	HepG2	liver
50	chr10:116292800-116294800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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