Variant report

Variant	rs16920504
Chromosome Location	chr9:104338094-104338095
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104332562..104334673-chr9:104335549..104338409,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10521057	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113384	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap]
rs12005425	0.83[CHB][hapmap]
rs12683273	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12684621	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12684773	0.86[CEU][hapmap];0.83[CHB][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12685862	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12686025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16920438	0.86[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16920447	0.93[MKK][hapmap]
rs16920479	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16920483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1929484	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs45572636	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742818	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743465	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4743471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57053192	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59111885	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59837044	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72743387	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72743390	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72743392	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72743394	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72743396	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72743397	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72745315	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72745318	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7867496	0.83[CHB][hapmap];0.97[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16920504	ZNF782	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104325200-104344400	Weak transcription	NHLF	lung
2	chr9:104325200-104350000	Weak transcription	HSMMtube	muscle
3	chr9:104327000-104338400	Weak transcription	Gastric	stomach
4	chr9:104327000-104344600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:104327400-104339600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:104327400-104348400	Weak transcription	Aorta	Aorta
7	chr9:104327600-104344400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:104327800-104338400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:104327800-104344400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:104328000-104342200	Weak transcription	Colon Smooth Muscle	Colon
11	chr9:104328400-104340600	Weak transcription	GM12878-XiMat	blood
12	chr9:104329000-104338800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr9:104329400-104338200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr9:104330200-104338600	Weak transcription	Colonic Mucosa	Colon
15	chr9:104331800-104344600	Weak transcription	HSMM	muscle
16	chr9:104332400-104338800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:104332400-104344600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:104332800-104340600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr9:104333000-104340600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr9:104333000-104342200	Weak transcription	Spleen	Spleen
21	chr9:104333000-104342400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:104333000-104344400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:104333000-104344400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:104333000-104344800	Weak transcription	A549	lung
25	chr9:104333400-104340000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr9:104333400-104340600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:104333400-104340800	Weak transcription	Primary B cells from cord blood	blood
28	chr9:104333400-104342400	Weak transcription	Fetal Stomach	stomach
29	chr9:104335200-104340600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:104335200-104344600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:104335400-104340600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:104335400-104344600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr9:104335400-104344800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr9:104335600-104340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:104335600-104340600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:104335600-104340800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:104335600-104344400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:104335600-104344600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:104335600-104346000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:104335800-104340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr9:104335800-104340800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:104336000-104340600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:104336200-104338800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr9:104336400-104338200	Enhancers	Fetal Brain Female	brain
45	chr9:104336600-104340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:104337000-104338200	Enhancers	Liver	Liver
47	chr9:104337400-104338400	Enhancers	Stomach Mucosa	stomach
48	chr9:104337600-104338400	Enhancers	HepG2	liver
49	chr9:104337800-104339200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr9:104337800-104339800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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