Variant report

Variant	rs35141782
Chromosome Location	chr9:78990145-78990146
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11144860	0.97[EUR][1000 genomes]
rs11791134	0.97[EUR][1000 genomes]
rs13284427	0.84[EUR][1000 genomes]
rs13284503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13286468	0.97[EUR][1000 genomes]
rs13289362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13290389	0.97[EUR][1000 genomes]
rs13291010	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13292857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13295158	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs13295871	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13297827	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13298404	0.97[EUR][1000 genomes]
rs13299207	0.97[EUR][1000 genomes]
rs17721472	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17777982	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34037675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34046058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34283683	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34286732	0.87[EUR][1000 genomes]
rs34307519	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34380148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34434749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34571197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34695412	0.97[EUR][1000 genomes]
rs34922670	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34990453	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs35012067	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs35031885	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35089043	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];0.97[EUR][1000 genomes]
rs35184004	0.84[EUR][1000 genomes]
rs35207397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35242982	0.97[EUR][1000 genomes]
rs35363570	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs35432738	0.90[EUR][1000 genomes]
rs35800025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35862905	0.84[EUR][1000 genomes]
rs35968404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36036209	0.84[EUR][1000 genomes]
rs58998344	0.81[EUR][1000 genomes]
rs7046651	0.97[EUR][1000 genomes]
rs71509867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71509868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71509870	0.97[EUR][1000 genomes]
rs71509872	0.97[EUR][1000 genomes]
rs71509873	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs71509874	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs71509875	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs71509878	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs71509879	1.00[AFR][1000 genomes];0.90[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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78984600-78993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:78986000-78990400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:78986800-78990400	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr9:78986800-78990600	Enhancers	Liver	Liver
6	chr9:78986800-78990800	Enhancers	Fetal Intestine Large	intestine
7	chr9:78986800-78990800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr9:78986800-78991000	Enhancers	Fetal Stomach	stomach
9	chr9:78987000-78990200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr9:78987000-78990600	Enhancers	Colon Smooth Muscle	Colon
11	chr9:78987000-78990600	Enhancers	Fetal Intestine Small	intestine
12	chr9:78987000-78990600	Enhancers	HepG2	liver
13	chr9:78987000-78991000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:78987200-78990400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:78987200-78991200	Enhancers	Stomach Mucosa	stomach
16	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:78988000-78990400	Enhancers	Fetal Muscle Leg	muscle
18	chr9:78988200-78993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:78988200-79002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:78988200-79003200	Weak transcription	HSMMtube	muscle
21	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
22	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
23	chr9:78988400-78990200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:78988400-78999000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr9:78988400-78999000	Weak transcription	Spleen	Spleen
26	chr9:78988400-78999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:78988400-79002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:78988600-78994200	Weak transcription	HMEC	breast
29	chr9:78988600-79001000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:78988600-79001000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:78988600-79002400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:78988800-78999800	Weak transcription	Brain Anterior Caudate	brain
35	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
36	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
37	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr9:78989000-78990400	Enhancers	Pancreas	Pancrea
39	chr9:78989000-78998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:78989000-78999800	Weak transcription	GM12878-XiMat	blood
41	chr9:78989000-79000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:78989000-79000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:78989200-78990600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr9:78989200-78990800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:78989200-78997800	Weak transcription	Ovary	ovary
46	chr9:78989400-78990400	Enhancers	Lung	lung
47	chr9:78989400-78990600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr9:78989400-78990600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:78989400-78990600	Enhancers	Rectal Smooth Muscle	rectum
50	chr9:78989400-78990600	Enhancers	NH-A	brain

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