Variant report

Variant	rs10739778
Chromosome Location	chr9:101875789-101875790
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101875608..101878128-chr9:101899514..101901966,2	K562	blood:
2	chr9:101834831..101839915-chr9:101875600..101879100,5	K562	blood:
3	chr9:101875664..101877877-chr9:101897071..101898718,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10733708	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10733709	0.82[ASN][1000 genomes]
rs10760667	0.85[ASN][1000 genomes]
rs10760668	0.84[ASN][1000 genomes]
rs10760669	0.86[ASN][1000 genomes]
rs10760670	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs10760671	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10760672	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10760673	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10760674	0.81[ASN][1000 genomes]
rs10819635	0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]
rs10819636	0.82[ASN][1000 genomes]
rs10819638	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10819640	0.81[ASN][1000 genomes]
rs10988706	0.81[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10988709	0.82[ASN][1000 genomes]
rs10988713	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs10988715	0.82[ASN][1000 genomes]
rs10988716	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10988717	0.81[ASN][1000 genomes]
rs10988723	0.81[ASN][1000 genomes]
rs11568752	0.82[ASN][1000 genomes]
rs12346650	0.82[YRI][hapmap]
rs12685571	0.82[ASN][1000 genomes]
rs12686783	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1571589	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs1590	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1626340	0.90[ASN][1000 genomes]
rs1699413	0.83[ASN][1000 genomes]
rs1888223	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1888225	0.82[ASN][1000 genomes]
rs1973518	0.81[ASN][1000 genomes]
rs2026811	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs334348	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs334349	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs334351	0.85[ASN][1000 genomes]
rs334353	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs334354	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs334355	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs334362	0.82[ASN][1000 genomes]
rs334363	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs334364	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs334365	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs334366	0.81[ASN][1000 genomes]
rs334367	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs334370	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs334371	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs367568	0.92[ASN][1000 genomes]
rs3739798	0.82[ASN][1000 genomes]
rs383496	0.92[ASN][1000 genomes]
rs401186	0.92[ASN][1000 genomes]
rs597457	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6478972	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs6478973	0.86[ASN][1000 genomes]
rs7022989	0.85[CHB][hapmap]
rs7031302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7031309	0.99[ASN][1000 genomes]
rs7042852	0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs7043624	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7874221	0.91[JPT][hapmap];0.86[ASN][1000 genomes]

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	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv893619	chr9:101835165-101936231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10739778	ZNF782	cis	cerebellum	SCAN
rs10739778	LOC286359	cis	parietal	SCAN
rs10739778	TGFBR1	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101868400-101881400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:101868400-101896400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:101868600-101889800	Weak transcription	Ovary	ovary
4	chr9:101868600-101894400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr9:101868800-101875800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr9:101869200-101881600	Weak transcription	Fetal Intestine Small	intestine
7	chr9:101869200-101884800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:101869400-101876000	Weak transcription	Stomach Mucosa	stomach
9	chr9:101869400-101876800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:101869400-101876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:101869600-101879400	Weak transcription	Placenta	Placenta
12	chr9:101869800-101884800	Weak transcription	A549	lung
13	chr9:101870000-101876200	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:101870000-101876400	Weak transcription	Liver	Liver
15	chr9:101870000-101879800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:101870000-101908600	Weak transcription	Brain Germinal Matrix	brain
17	chr9:101870200-101876000	Weak transcription	NH-A	brain
18	chr9:101870200-101878200	Weak transcription	Fetal Lung	lung
19	chr9:101870200-101879200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:101870400-101876200	Weak transcription	Brain Anterior Caudate	brain
21	chr9:101870400-101881400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:101870600-101881200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr9:101870600-101889800	Weak transcription	NHLF	lung
24	chr9:101870800-101878400	Weak transcription	Fetal Stomach	stomach
25	chr9:101871000-101876600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:101871400-101878200	Weak transcription	Fetal Brain Male	brain
27	chr9:101872000-101877000	Enhancers	Primary B cells from cord blood	blood
28	chr9:101872000-101877200	Weak transcription	HMEC	breast
29	chr9:101872200-101878200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:101872400-101876200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:101872400-101876200	Weak transcription	HSMMtube	muscle
32	chr9:101872400-101876800	Weak transcription	NHDF-Ad	bronchial
33	chr9:101872400-101878400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:101872600-101881200	Weak transcription	HSMM	muscle
35	chr9:101872600-101887800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr9:101872800-101877800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:101873000-101877400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:101873200-101877200	Weak transcription	Fetal Brain Female	brain
39	chr9:101873400-101878200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:101873800-101875800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:101873800-101876000	Enhancers	Fetal Thymus	thymus
42	chr9:101873800-101876400	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr9:101873800-101879200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr9:101874000-101875800	Enhancers	Primary B cells from peripheral blood	blood
45	chr9:101874000-101876200	Enhancers	Thymus	Thymus
46	chr9:101874000-101877800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:101874000-101877800	Enhancers	Adipose Nuclei	Adipose
48	chr9:101874000-101878000	Enhancers	Colon Smooth Muscle	Colon
49	chr9:101874000-101878400	Enhancers	Rectal Smooth Muscle	rectum
50	chr9:101874000-101878800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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