Variant report

Variant	rs10119978
Chromosome Location	chr9:116707820-116707821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116707223..116710923-chr9:116723048..116727308,3	MCF-7	breast:
2	chr9:116704077..116708028-chr9:116709899..116712780,3	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10448275	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10448276	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10513223	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs10739396	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs10759664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10759666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10817536	0.94[EUR][1000 genomes]
rs10817537	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817538	0.81[EUR][1000 genomes]
rs10817539	1.00[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10817541	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10982008	0.95[EUR][1000 genomes]
rs10982009	0.90[ASN][1000 genomes]
rs10982015	0.81[CHB][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10982017	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12551141	0.95[CHB][hapmap]
rs1330166	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1536962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1544102	0.81[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1888161	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[EUR][1000 genomes]
rs2026143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2418261	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2761688	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2773396	0.85[CEU][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2900570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2900571	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4979295	0.80[GIH][hapmap]
rs4979298	0.95[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap]
rs4979307	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7032101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7038501	0.80[GIH][hapmap]
rs7046776	0.82[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7867998	1.00[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7869027	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs814680	0.96[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs814686	0.86[ASN][1000 genomes]
rs814696	0.85[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs871806	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs871808	1.00[CEU][hapmap];0.81[YRI][hapmap];0.95[EUR][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	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10119978	PALM2-AKAP2	cis	parietal	SCAN
rs10119978	ZFP37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116691800-116709000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:116692000-116719400	Weak transcription	HMEC	breast
3	chr9:116692400-116716800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:116692400-116717200	Weak transcription	A549	lung
5	chr9:116693800-116714200	Weak transcription	Fetal Kidney	kidney
6	chr9:116695600-116711600	Weak transcription	Liver	Liver
7	chr9:116695800-116708800	Weak transcription	Pancreas	Pancrea
8	chr9:116695800-116716000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:116696000-116714800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:116696200-116719800	Weak transcription	Gastric	stomach
11	chr9:116697600-116715000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:116698200-116708200	Weak transcription	Fetal Intestine Small	intestine
13	chr9:116698400-116708800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:116703600-116714600	Weak transcription	NH-A	brain
15	chr9:116703600-116719800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:116703800-116716000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:116703800-116716600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:116704000-116708200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:116704200-116713000	Strong transcription	Fetal Stomach	stomach
20	chr9:116704200-116715400	Weak transcription	NHLF	lung
21	chr9:116704400-116709000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:116704400-116714400	Weak transcription	NHDF-Ad	bronchial
23	chr9:116704400-116714600	Weak transcription	HSMMtube	muscle
24	chr9:116704400-116714600	Weak transcription	Osteobl	bone
25	chr9:116704400-116717000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:116704600-116712600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr9:116704600-116716400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:116704800-116714600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:116705200-116714000	Weak transcription	HUVEC	blood vessel
30	chr9:116705400-116712000	Weak transcription	Brain Germinal Matrix	brain
31	chr9:116705400-116714600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:116705600-116712400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:116705800-116708800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:116705800-116708800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:116705800-116708800	Weak transcription	Lung	lung
36	chr9:116705800-116709000	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:116705800-116709800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:116705800-116710200	Weak transcription	Spleen	Spleen
39	chr9:116705800-116715800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:116705800-116716200	Weak transcription	Right Atrium	heart
41	chr9:116706200-116716400	Weak transcription	Aorta	Aorta
42	chr9:116706200-116716800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:116706400-116709400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:116706400-116709800	Weak transcription	Ovary	ovary
45	chr9:116706800-116717000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:116707600-116708800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:116707600-116708800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:116707800-116708400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:116707800-116714600	Weak transcription	HSMM	muscle
50	chr9:116707800-116717000	Weak transcription	Fetal Lung	lung

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