Variant report

Variant	rs35800025
Chromosome Location	chr9:79006054-79006055
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	chr9:78999922..79001730-chr9:79004371..79006300,2	MCF-7	breast:
2	chr9:79003083..79006280-chr9:79008607..79011361,3	K562	blood:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11144860	1.00[EUR][1000 genomes]
rs11791134	1.00[EUR][1000 genomes]
rs13284427	0.87[EUR][1000 genomes]
rs13284503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13286468	1.00[EUR][1000 genomes]
rs13289362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13290389	1.00[EUR][1000 genomes]
rs13291010	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13292857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13295158	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13295871	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13297827	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13298404	1.00[EUR][1000 genomes]
rs13299207	1.00[EUR][1000 genomes]
rs17721472	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17777982	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34037675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34046058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34283683	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34286732	0.90[EUR][1000 genomes]
rs34307519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34380148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34434749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34571197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34695412	1.00[EUR][1000 genomes]
rs34922670	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34990453	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35012067	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35031885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35089043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35141782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35171014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35184004	0.87[EUR][1000 genomes]
rs35207397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35242982	1.00[EUR][1000 genomes]
rs35363570	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35432738	0.93[EUR][1000 genomes]
rs35862905	0.87[EUR][1000 genomes]
rs35968404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36036209	0.87[EUR][1000 genomes]
rs58998344	0.84[EUR][1000 genomes]
rs7046651	1.00[EUR][1000 genomes]
rs71509867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71509868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71509870	1.00[EUR][1000 genomes]
rs71509872	1.00[EUR][1000 genomes]
rs71509873	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71509874	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71509875	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71509878	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs71509879	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
4	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
5	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:78990200-79007800	Weak transcription	Fetal Brain Male	brain
10	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
11	chr9:78990400-79008200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:78990400-79008400	Weak transcription	Fetal Kidney	kidney
13	chr9:78990600-79008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:78990600-79008400	Weak transcription	Fetal Lung	lung
15	chr9:78990600-79008400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:78990800-79008400	Weak transcription	NHLF	lung
17	chr9:78992200-79008600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:78995200-79007600	Weak transcription	Gastric	stomach
19	chr9:78995200-79007600	Weak transcription	HMEC	breast
20	chr9:78995200-79007600	Weak transcription	NHEK	skin
21	chr9:78995200-79008400	Weak transcription	Stomach Mucosa	stomach
22	chr9:78995200-79008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr9:78996000-79008400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:78997000-79007600	Weak transcription	Lung	lung
25	chr9:78997600-79008400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:78997800-79008400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:78998400-79008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:78998800-79007800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:78998800-79008600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:78999000-79007600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr9:78999200-79008400	Weak transcription	NH-A	brain
32	chr9:78999400-79008600	Weak transcription	Spleen	Spleen
33	chr9:78999600-79006600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:78999800-79007600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:79000000-79007000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr9:79000200-79007400	Weak transcription	Colonic Mucosa	Colon
37	chr9:79000200-79008400	Weak transcription	Pancreas	Pancrea
38	chr9:79000400-79008400	Weak transcription	Thymus	Thymus
39	chr9:79002000-79008400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:79002600-79007400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:79002800-79006400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:79003000-79007400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:79003000-79007400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:79003000-79007600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:79003000-79007800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:79003000-79008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:79003000-79008400	Weak transcription	Aorta	Aorta
48	chr9:79003000-79008400	Weak transcription	Left Ventricle	heart
49	chr9:79003000-79008600	Weak transcription	Esophagus	oesophagus
50	chr9:79003200-79006800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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