Variant report

Variant	rs323885
Chromosome Location	chr3:51966504-51966505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51965101..51968149-chr3:51999583..52001549,3	K562	blood:
2	chr3:51965258..51969010-chr3:51974469..51977350,4	MCF-7	breast:
3	chr3:51963363..51966858-chr3:51969595..51972512,3	MCF-7	breast:
4	chr3:51965268..51966956-chr3:51968689..51971513,2	MCF-7	breast:
5	chr3:51962409..51965326-chr3:51965787..51967920,2	K562	blood:
6	chr3:51965328..51968985-chr3:51969844..51971863,5	K562	blood:

Variant related genes	Relation type
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000090097	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11926611	1.00[ASN][1000 genomes]
rs1566941	0.89[ASN][1000 genomes]
rs1876052	0.89[ASN][1000 genomes]
rs188953	0.87[AFR][1000 genomes]
rs2271069	0.89[ASN][1000 genomes]
rs323864	0.98[ASN][1000 genomes]
rs323868	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323871	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323873	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323874	1.00[ASN][1000 genomes]
rs323879	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323881	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323886	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323887	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323893	1.00[ASN][1000 genomes]
rs323894	1.00[ASN][1000 genomes]
rs323895	1.00[ASN][1000 genomes]
rs323898	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755797	0.89[ASN][1000 genomes]
rs3774344	0.89[ASN][1000 genomes]
rs411209	1.00[ASN][1000 genomes]
rs4986825	0.89[ASN][1000 genomes]
rs56715917	0.89[ASN][1000 genomes]
rs61087263	0.89[ASN][1000 genomes]
rs6446166	0.85[ASN][1000 genomes]
rs7614743	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51950600-51967000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:51960600-51974400	Weak transcription	Fetal Brain Male	brain
3	chr3:51961400-51966600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:51962000-51966800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:51962200-51966600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:51962600-51966600	Weak transcription	Spleen	Spleen
7	chr3:51962600-51966800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:51962600-51973200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:51962800-51966600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:51962800-51966600	Weak transcription	Gastric	stomach
11	chr3:51962800-51966800	Weak transcription	NHLF	lung
12	chr3:51963400-51966600	Weak transcription	Fetal Brain Female	brain
13	chr3:51963400-51966800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:51963600-51966600	Weak transcription	Primary T cells from cord blood	blood
15	chr3:51963600-51966600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:51963600-51966600	Weak transcription	Esophagus	oesophagus
17	chr3:51963600-51966800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:51963600-51966800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:51963600-51966800	Weak transcription	Fetal Lung	lung
20	chr3:51963800-51966600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:51963800-51966600	Weak transcription	Brain Angular Gyrus	brain
22	chr3:51963800-51966600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:51963800-51966800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:51963800-51966800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:51963800-51967000	Weak transcription	A549	lung
26	chr3:51963800-51974400	Weak transcription	Right Atrium	heart
27	chr3:51964000-51968000	Weak transcription	HUVEC	blood vessel
28	chr3:51964000-51972800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:51964200-51966600	Weak transcription	Left Ventricle	heart
30	chr3:51964200-51966800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:51964400-51966600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr3:51964400-51966600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:51964400-51966800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:51964400-51966800	Weak transcription	Placenta	Placenta
35	chr3:51964400-51966800	Weak transcription	HMEC	breast
36	chr3:51964400-51972600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:51964400-51973200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:51964400-51973600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:51964400-51973600	Strong transcription	Thymus	Thymus
40	chr3:51964600-51966600	Weak transcription	Dnd41	blood
41	chr3:51964600-51966800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr3:51964600-51967000	Weak transcription	Colonic Mucosa	Colon
43	chr3:51964600-51971400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:51964600-51972800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:51964800-51966600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:51964800-51966600	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:51964800-51966600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:51964800-51966800	Weak transcription	Fetal Intestine Large	intestine
49	chr3:51964800-51973600	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:51965000-51966600	Weak transcription	Rectal Mucosa Donor 31	rectum

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