Variant report

Variant	rs323863
Chromosome Location	chr3:52027072-52027073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11916396	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11926611	0.84[YRI][hapmap]
rs2015691	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];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]
rs323862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323865	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs323868	1.00[MEX][hapmap];0.80[MKK][hapmap];0.90[AMR][1000 genomes]
rs323873	1.00[MEX][hapmap]
rs323874	1.00[MEX][hapmap]
rs323879	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs323887	1.00[MEX][hapmap]
rs323890	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323893	0.84[YRI][hapmap]
rs323894	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs323895	0.84[YRI][hapmap]
rs323897	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323898	1.00[MEX][hapmap];0.80[MKK][hapmap]
rs379462	0.85[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	1.00[YRI][hapmap];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	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs433823	1.00[CHD][hapmap];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	0.83[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs82854	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9840336	1.00[CHD][hapmap]

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	chr3:52018400-52028400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:52018400-52028400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:52021200-52028000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:52022400-52028000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:52023800-52028600	Weak transcription	Right Atrium	heart
13	chr3:52024000-52027600	Strong transcription	Fetal Stomach	stomach
14	chr3:52025400-52027400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:52025400-52027600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:52025400-52027800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:52025400-52028200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:52025400-52028200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:52025400-52028200	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:52025400-52028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:52025400-52028400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr3:52025400-52028400	Genic enhancers	Fetal Intestine Large	intestine
23	chr3:52025400-52028600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:52025400-52028600	Strong transcription	Rectal Smooth Muscle	rectum
25	chr3:52025600-52027600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:52025600-52027800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr3:52025600-52028000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:52025600-52028200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:52025600-52028200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:52025600-52028200	Strong transcription	Lung	lung
31	chr3:52025600-52028200	Weak transcription	Stomach Mucosa	stomach
32	chr3:52025600-52028200	Genic enhancers	HepG2	liver
33	chr3:52025600-52028600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:52025600-52028600	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr3:52025600-52028600	Strong transcription	Thymus	Thymus
36	chr3:52025800-52027200	Genic enhancers	A549	lung
37	chr3:52025800-52027600	Strong transcription	Spleen	Spleen
38	chr3:52025800-52028000	Strong transcription	Fetal Intestine Small	intestine
39	chr3:52025800-52028200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:52025800-52028200	Strong transcription	Right Ventricle	heart
41	chr3:52025800-52028400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:52025800-52029000	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr3:52025800-52029200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr3:52026000-52027200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:52026000-52027200	Strong transcription	NHDF-Ad	bronchial
46	chr3:52026000-52028200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52026000-52028200	Strong transcription	Primary B cells from cord blood	blood
48	chr3:52026000-52028200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:52026000-52028200	Strong transcription	Left Ventricle	heart
50	chr3:52026000-52028400	Genic enhancers	Primary hematopoietic stem cells	blood

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