Variant report

Variant	rs323862
Chromosome Location	chr3:52026775-52026776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52026551..52028922-chr3:52257127..52259842,2	K562	blood:
2	chr12:46122158..46123204-chr3:52026001..52026840,3	NB4	blood:
3	chr3:52025976..52031164-chr3:52185902..52190126,6	K562	blood:
4	chr3:51974147..51980389-chr3:52024451..52030996,12	K562	blood:
5	chr3:52026096..52028947-chr3:52173334..52176505,3	K562	blood:
6	chr3:51987614..51990073-chr3:52025987..52029912,3	K562	blood:
7	chr3:52006271..52012102-chr3:52024917..52032079,14	MCF-7	breast:
8	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:

No data

Variant related genes	Relation type
ENSG00000114779	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000272762	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000114786	Chromatin interaction
ENSG00000180929	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000248487	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11916396	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2015691	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323859	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs323861	0.94[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs323897	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs379462	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs404527	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	0.90[AFR][1000 genomes]
rs433823	1.00[ASN][1000 genomes]
rs451154	0.89[AMR][1000 genomes]
rs72964028	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72964029	1.00[ASN][1000 genomes]
rs7432986	0.81[AFR][1000 genomes]
rs82854	0.82[AFR][1000 genomes];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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52017800-52027600	Weak transcription	Fetal Brain Male	brain
2	chr3:52017800-52028200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:52017800-52028200	Weak transcription	Aorta	Aorta
4	chr3:52017800-52028600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:52018000-52028000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:52018200-52027400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:52018200-52027600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:52018400-52026800	Weak transcription	Fetal Kidney	kidney
9	chr3:52018400-52026800	Weak transcription	Psoas Muscle	Psoas
10	chr3:52018400-52028400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:52018400-52028400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:52019200-52026800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:52020600-52026800	Weak transcription	Pancreas	Pancrea
14	chr3:52021200-52028000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:52022400-52028000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:52023800-52028600	Weak transcription	Right Atrium	heart
17	chr3:52024000-52027600	Strong transcription	Fetal Stomach	stomach
18	chr3:52025400-52026800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:52025400-52026800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:52025400-52026800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:52025400-52026800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:52025400-52026800	Strong transcription	NHEK	skin
23	chr3:52025400-52027000	Genic enhancers	H1 Cell Line	embryonic stem cell
24	chr3:52025400-52027000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:52025400-52027000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:52025400-52027000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:52025400-52027400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52025400-52027600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:52025400-52027800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:52025400-52028200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:52025400-52028200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:52025400-52028200	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:52025400-52028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:52025400-52028400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:52025400-52028400	Genic enhancers	Fetal Intestine Large	intestine
36	chr3:52025400-52028600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:52025400-52028600	Strong transcription	Rectal Smooth Muscle	rectum
38	chr3:52025600-52027000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:52025600-52027000	Strong transcription	Ovary	ovary
40	chr3:52025600-52027600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:52025600-52027800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr3:52025600-52028000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
43	chr3:52025600-52028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:52025600-52028200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:52025600-52028200	Strong transcription	Lung	lung
46	chr3:52025600-52028200	Weak transcription	Stomach Mucosa	stomach
47	chr3:52025600-52028200	Genic enhancers	HepG2	liver
48	chr3:52025600-52028600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:52025600-52028600	Genic enhancers	Duodenum Mucosa	Duodenum
50	chr3:52025600-52028600	Strong transcription	Thymus	Thymus

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