Variant report

Variant	rs28529075
Chromosome Location	chr3:196346791-196346792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196344291..196346990-chr3:196361861..196363448,2	K562	blood:
2	chr3:196344681..196346820-chr3:196413702..196415608,2	MCF-7	breast:
3	chr3:196345698..196350992-chr3:196355970..196361124,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232065	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11717827	0.81[ASN][1000 genomes]
rs11719704	0.86[ASN][1000 genomes]
rs13098252	0.86[ASN][1000 genomes]
rs28579649	0.86[ASN][1000 genomes]
rs28664893	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34180254	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35107793	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35918545	0.81[ASN][1000 genomes]
rs4605582	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73081083	0.86[ASN][1000 genomes]
rs7617545	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7653474	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9816722	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9826948	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827118	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853127	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9882393	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv878188	chr3:196312124-196553867	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196337000-196347000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:196337200-196347000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:196339600-196346800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:196339600-196347000	Weak transcription	Primary B cells from cord blood	blood
5	chr3:196339600-196347000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:196339600-196347000	Weak transcription	Lung	lung
7	chr3:196339600-196354800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:196339800-196351000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:196340000-196347200	Weak transcription	Spleen	Spleen
10	chr3:196340600-196350200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:196340800-196346800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:196342400-196347200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:196343000-196349200	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:196343400-196351000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:196344200-196347600	Enhancers	Fetal Intestine Small	intestine
16	chr3:196344400-196346800	Weak transcription	GM12878-XiMat	blood
17	chr3:196344600-196346800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:196344600-196350200	Weak transcription	Primary T cells from cord blood	blood
19	chr3:196344600-196351000	Weak transcription	Thymus	Thymus
20	chr3:196345400-196351200	Enhancers	Fetal Thymus	thymus
21	chr3:196345600-196347000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr3:196345600-196347600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:196345600-196347600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:196345600-196347800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:196345800-196347000	Enhancers	Colon Smooth Muscle	Colon
26	chr3:196345800-196347200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr3:196345800-196347200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:196345800-196347600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:196345800-196347600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:196345800-196347800	Enhancers	Rectal Smooth Muscle	rectum
31	chr3:196346000-196347000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:196346000-196347000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:196346000-196347000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:196346000-196347000	Enhancers	HepG2	liver
35	chr3:196346000-196347200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:196346000-196347400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr3:196346000-196347400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:196346000-196347400	Enhancers	Fetal Intestine Large	intestine
39	chr3:196346000-196347600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:196346000-196347600	Enhancers	K562	blood
41	chr3:196346000-196347800	Enhancers	HUVEC	blood vessel
42	chr3:196346000-196348600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:196346200-196346800	Weak transcription	Right Atrium	heart
44	chr3:196346200-196347000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:196346200-196347000	Weak transcription	Adipose Nuclei	Adipose
46	chr3:196346200-196347000	Weak transcription	Brain Anterior Caudate	brain
47	chr3:196346200-196347000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:196346200-196347200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:196346200-196347200	Enhancers	Brain Angular Gyrus	brain
50	chr3:196346200-196347200	Weak transcription	Placenta	Placenta

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