Variant report

Variant	rs9843876
Chromosome Location	chr3:196223899-196223900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196215210..196217235-chr3:196222277..196224657,2	K562	blood:
2	chr3:196221498..196224147-chr3:196224892..196227326,3	K562	blood:
3	chr3:196217384..196220368-chr3:196221757..196224156,3	K562	blood:
4	chr3:196221948..196224037-chr3:196229901..196232321,3	K562	blood:

Variant related genes	Relation type
ENSG00000163961	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11707744	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12632592	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13099664	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34547573	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4244200	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4916497	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4916498	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5016648	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55997345	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6772271	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7430950	0.85[ASN][1000 genomes]
rs7433483	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9837568	0.93[ASN][1000 genomes]
rs9844068	0.94[ASN][1000 genomes]
rs9856006	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864836	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9869437	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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	45 gene(s)	inside rSNPs	diseases
4	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
10	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9843876	UBXD7	Cis_1M	lymphoblastoid	RTeQTL
rs9843876	FBXO45	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196199400-196227000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:196210800-196226000	Weak transcription	Psoas Muscle	Psoas
3	chr3:196213000-196226800	Weak transcription	Fetal Kidney	kidney
4	chr3:196213400-196225800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:196213800-196226600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:196214200-196225000	Weak transcription	Ovary	ovary
7	chr3:196214200-196225400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:196214200-196225400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:196214200-196226000	Weak transcription	A549	lung
10	chr3:196214400-196225000	Weak transcription	Small Intestine	intestine
11	chr3:196214400-196225800	Weak transcription	HSMMtube	muscle
12	chr3:196214400-196225800	Weak transcription	NHEK	skin
13	chr3:196214400-196226000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:196214400-196226000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:196214400-196226000	Weak transcription	Esophagus	oesophagus
16	chr3:196214400-196226000	Weak transcription	Gastric	stomach
17	chr3:196214400-196226200	Weak transcription	Right Ventricle	heart
18	chr3:196214400-196226400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:196214400-196226600	Weak transcription	Aorta	Aorta
20	chr3:196214400-196226800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:196214400-196226800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:196214400-196226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:196214400-196226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:196214400-196226800	Weak transcription	Brain Anterior Caudate	brain
25	chr3:196214400-196226800	Weak transcription	Pancreas	Pancrea
26	chr3:196214400-196227000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:196214400-196227000	Weak transcription	Fetal Lung	lung
28	chr3:196214400-196227000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:196214400-196228200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:196214600-196224600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:196214600-196225400	Weak transcription	HMEC	breast
32	chr3:196214600-196226000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:196214600-196226000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:196214600-196226000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:196214600-196226000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:196214600-196226000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:196214600-196226000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:196214600-196226200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:196214600-196226200	Weak transcription	Fetal Brain Male	brain
40	chr3:196214600-196226400	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:196214600-196226400	Weak transcription	Spleen	Spleen
42	chr3:196214600-196226800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:196214600-196226800	Weak transcription	Colonic Mucosa	Colon
44	chr3:196214600-196226800	Weak transcription	Fetal Intestine Large	intestine
45	chr3:196214600-196226800	Weak transcription	Lung	lung
46	chr3:196214800-196225000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:196214800-196226000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:196214800-196227200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:196215000-196225400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:196215000-196225800	Weak transcription	Osteobl	bone

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