Variant report

Variant	rs9790982
Chromosome Location	chr5:14776585-14776586
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	chr5:14774249..14779166-chr5:14785300..14788951,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154122	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1061813	0.93[CHB][hapmap];0.81[ASN][1000 genomes]
rs11133799	0.83[ASN][1000 genomes]
rs12653321	0.83[ASN][1000 genomes]
rs13155894	0.82[ASN][1000 genomes]
rs1353258	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2453316	0.82[ASN][1000 genomes]
rs258218	0.84[ASN][1000 genomes]
rs258219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258222	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs258224	0.90[ASN][1000 genomes]
rs258225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs258226	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs258227	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs258228	0.90[ASN][1000 genomes]
rs258231	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs25957	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28005	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28108	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs30615	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs31909	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs31912	0.93[CHB][hapmap];0.84[ASN][1000 genomes]
rs31933	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31990	0.86[CHB][hapmap]
rs33102	0.82[ASN][1000 genomes]
rs39636	0.82[ASN][1000 genomes]
rs39916	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs573116	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs826352	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs879253	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][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	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv948447	chr5:14771247-14852610	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9790982	DNAH5	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14729200-14791000	Weak transcription	Small Intestine	intestine
2	chr5:14746000-14790200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:14752200-14776600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:14753400-14777000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:14753600-14790000	Weak transcription	Ovary	ovary
6	chr5:14753600-14801600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:14756800-14779000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr5:14756800-14780200	Weak transcription	Fetal Stomach	stomach
9	chr5:14756800-14781200	Weak transcription	Thymus	Thymus
10	chr5:14758800-14783800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:14759200-14790200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:14761000-14777800	Weak transcription	HSMMtube	muscle
13	chr5:14766600-14780000	Weak transcription	Fetal Intestine Large	intestine
14	chr5:14767400-14809800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr5:14768400-14789800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:14768600-14779400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:14768600-14790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:14768600-14790200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr5:14768600-14790200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:14768600-14790200	Weak transcription	Dnd41	blood
21	chr5:14768800-14779000	Weak transcription	Primary T cells from cord blood	blood
22	chr5:14769000-14780800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:14769200-14789400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:14769400-14778800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:14769400-14790600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr5:14769400-14790600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr5:14770200-14777600	Weak transcription	Fetal Brain Male	brain
28	chr5:14771600-14777400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:14772600-14778000	Enhancers	HepG2	liver
30	chr5:14773800-14777800	Weak transcription	Aorta	Aorta
31	chr5:14773800-14778000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:14774000-14778200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:14774000-14780800	Weak transcription	Brain Angular Gyrus	brain
34	chr5:14774200-14776800	Weak transcription	Brain Germinal Matrix	brain
35	chr5:14774200-14777600	Weak transcription	Fetal Brain Female	brain
36	chr5:14774200-14777800	Enhancers	A549	lung
37	chr5:14774400-14778200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:14775000-14776800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:14775200-14779800	Strong transcription	Fetal Intestine Small	intestine
40	chr5:14775400-14777200	Enhancers	Stomach Mucosa	stomach
41	chr5:14775600-14776600	Enhancers	Colonic Mucosa	Colon
42	chr5:14775600-14776600	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr5:14775600-14777200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr5:14775600-14778400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:14775600-14779600	Enhancers	Left Ventricle	heart
46	chr5:14775600-14783800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr5:14775800-14776600	Enhancers	NH-A	brain
48	chr5:14775800-14776800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:14775800-14776800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr5:14775800-14776800	Enhancers	Fetal Heart	heart

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