Variant report

Variant	rs9853777
Chromosome Location	chr3:196293516-196293517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196292428..196296416-chr3:196668494..196671676,5	MCF-7	breast:
2	chr3:196228489..196231887-chr3:196292830..196296417,3	MCF-7	breast:
3	chr3:196292826..196295435-chr3:196358532..196360090,2	K562	blood:
4	chr3:196277565..196279169-chr3:196291112..196294085,2	K562	blood:

Variant related genes	Relation type
ENSG00000114503	Chromatin interaction
ENSG00000232065	Chromatin interaction
ENSG00000163961	Chromatin interaction
ENSG00000270170	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11185545	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1124996	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707537	0.89[EUR][1000 genomes]
rs11711594	0.83[AMR][1000 genomes]
rs1355533	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2054748	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2054749	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2054750	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2137193	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28479172	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2880030	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34292861	0.98[EUR][1000 genomes]
rs4916433	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs60668021	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6583317	0.80[AMR][1000 genomes]
rs6583318	0.85[AMR][1000 genomes]
rs66588136	0.82[AMR][1000 genomes]
rs7619117	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621684	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7626039	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9311	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9647412	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9647413	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9813420	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9814342	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9817377	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9828786	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9831225	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9843607	0.97[EUR][1000 genomes]
rs9848622	0.83[AMR][1000 genomes]
rs9868492	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	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
7	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv878187	chr3:196245603-196554790	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv491864	chr3:196263064-196468533	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv829828	chr3:196268121-196463641	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv1010643	chr3:196288064-196788645	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196276800-196293800	Weak transcription	HepG2	liver
2	chr3:196277600-196294200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:196277800-196293600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:196278000-196294400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:196278800-196294600	Weak transcription	Gastric	stomach
6	chr3:196279000-196294000	Weak transcription	Brain Anterior Caudate	brain
7	chr3:196279000-196294200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:196279200-196294000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:196279200-196294400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:196279400-196294200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:196279600-196294400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:196279800-196294400	Weak transcription	Right Ventricle	heart
13	chr3:196279800-196294600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:196280200-196294200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:196281600-196294600	Weak transcription	Psoas Muscle	Psoas
16	chr3:196281800-196293600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:196283400-196294600	Weak transcription	Fetal Brain Male	brain
18	chr3:196284600-196293800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:196284600-196294600	Weak transcription	Colonic Mucosa	Colon
20	chr3:196285000-196294400	Weak transcription	HSMM	muscle
21	chr3:196285400-196294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:196286200-196293800	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:196286200-196294200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:196286400-196294000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:196286400-196294600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:196287000-196294400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:196288000-196294200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:196288200-196294000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:196288200-196294000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:196288200-196294000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:196288200-196294200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:196288200-196294400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:196288200-196294400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:196288400-196293600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:196288400-196294000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:196288400-196294000	Weak transcription	Liver	Liver
37	chr3:196288400-196294000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:196288400-196294200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:196288400-196294200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:196288400-196294200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:196288400-196294200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:196288400-196294200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:196288400-196294200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:196288400-196294400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:196288400-196294400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:196288400-196294400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:196288400-196294400	Weak transcription	Brain Substantia Nigra	brain
48	chr3:196288400-196294400	Weak transcription	Fetal Brain Female	brain
49	chr3:196288400-196294400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:196288400-196294400	Weak transcription	Osteobl	bone

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