Variant report

Variant	rs11916396
Chromosome Location	chr3:52030357-52030358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESRRA	chr3:52028371-52030386	GM12878	blood:	n/a	n/a
2	REST	chr3:52029173-52030371	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr3:52030215-52030358	GM12878	blood:	n/a	n/a
4	CTCF	chr3:52030279-52030371	GM10266	blood:	n/a	n/a
5	POLR2A	chr3:52016082-52030443	HepG2	liver:	n/a	n/a
6	SREBP2	chr3:52029105-52030358	GM12878	blood:	n/a	n/a
7	MXI1	chr3:52028742-52030375	SK-N-SH	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52001556..52005448-chr3:52028528..52032420,5	MCF-7	breast:
2	chr3:51974644..51978429-chr3:52029121..52032128,7	MCF-7	breast:
3	chr3:52025976..52031164-chr3:52185902..52190126,6	K562	blood:
4	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
5	chr3:52005327..52011372-chr3:52027090..52031188,9	MCF-7	breast:
6	chr3:52029706..52030479-chr7:139044089..139044589,2	NB4	blood:
7	chr3:52028577..52031266-chr3:52230149..52233019,2	K562	blood:
8	chr3:52006271..52012102-chr3:52024917..52032079,14	MCF-7	breast:
9	chr3:51974392..51977854-chr3:52027120..52030701,3	MCF-7	breast:
10	chr3:52026823..52031380-chr3:52087204..52091486,4	K562	blood:
11	chr3:52028061..52031321-chr3:52088873..52092735,5	MCF-7	breast:

No data

Variant related genes	Relation type
RPL29	TF binding region
ENSG00000164086	Chromatin interaction
ENSG00000273391	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000023330	Chromatin interaction
ENSG00000248487	Chromatin interaction
ENSG00000146963	Chromatin interaction
ENSG00000272762	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000114779	Chromatin interaction
ENSG00000090097	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2015691	1.00[ASN][1000 genomes]
rs323858	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323859	0.89[AMR][1000 genomes]
rs323861	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323862	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323865	1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[ASN][1000 genomes]
rs323868	0.90[AMR][1000 genomes]
rs323879	0.90[AMR][1000 genomes]
rs323890	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	0.90[AMR][1000 genomes]
rs323897	1.00[ASN][1000 genomes]
rs379462	1.00[ASN][1000 genomes]
rs380788	1.00[ASN][1000 genomes]
rs403620	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs404527	1.00[ASN][1000 genomes]
rs433823	1.00[ASN][1000 genomes]
rs451154	0.89[AMR][1000 genomes]
rs72964028	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72964029	1.00[ASN][1000 genomes]
rs82854	0.89[AMR][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	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 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	chr3:52029000-52030400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:52029200-52030400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:52029200-52030400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr3:52029200-52030400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:52029200-52030400	Active TSS	Brain Angular Gyrus	brain
6	chr3:52029200-52030400	Active TSS	Fetal Intestine Large	intestine
7	chr3:52029200-52030400	Active TSS	Pancreas	Pancrea
8	chr3:52029400-52030400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:52029400-52030400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:52029400-52030400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:52029400-52030400	Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr3:52029400-52030400	Active TSS	Liver	Liver
13	chr3:52029400-52030400	Active TSS	Brain Cingulate Gyrus	brain
14	chr3:52029400-52030400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:52029400-52030400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr3:52029400-52030400	Active TSS	Thymus	Thymus
17	chr3:52029400-52030400	Active TSS	Osteobl	bone
18	chr3:52029600-52030400	Active TSS	Primary monocytes fromperipheralblood	blood
19	chr3:52029600-52030400	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:52029600-52030400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52029600-52030400	Active TSS	Adipose Nuclei	Adipose
22	chr3:52029600-52030400	Active TSS	Duodenum Mucosa	Duodenum
23	chr3:52029600-52030400	Active TSS	Fetal Muscle Leg	muscle
24	chr3:52029600-52030400	Active TSS	Placenta	Placenta
25	chr3:52029600-52030400	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:52029600-52030400	Active TSS	Rectal Smooth Muscle	rectum
27	chr3:52029800-52030400	Active TSS	Brain Anterior Caudate	brain
28	chr3:52029800-52030400	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr3:52029800-52030400	Active TSS	HepG2	liver
30	chr3:52030000-52030400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:52030000-52030400	Active TSS	Fetal Intestine Small	intestine
32	chr3:52030000-52030400	Flanking Active TSS	Dnd41	blood
33	chr3:52030000-52031200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:52030000-52031600	Weak transcription	K562	blood
35	chr3:52030000-52031800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:52030000-52031800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:52030000-52031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:52030000-52031800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:52030000-52031800	Weak transcription	HMEC	breast
40	chr3:52030000-52032000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:52030000-52032000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:52030000-52032000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:52030000-52032000	Weak transcription	HSMM	muscle
44	chr3:52030000-52032200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:52030000-52034200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:52030000-52034400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:52030000-52035600	Weak transcription	Esophagus	oesophagus
48	chr3:52030200-52030400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr3:52030200-52030400	Enhancers	Primary B cells from cord blood	blood
50	chr3:52030200-52030400	Enhancers	Primary B cells from peripheral blood	blood

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