Variant report

Variant	rs56223679
Chromosome Location	chr3:99602380-99602381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99601088..99603478-chr3:99611897..99614954,3	MCF-7	breast:
2	chr3:99596053..99600789-chr3:99601531..99605674,5	MCF-7	breast:
3	chr3:99599836..99602681-chr3:99604247..99606316,2	K562	blood:
4	chr3:99601766..99603960-chr3:99724495..99726434,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1038295	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10804762	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	0.83[ASN][1000 genomes]
rs12486901	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489030	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	0.84[EUR][1000 genomes]
rs12493124	0.93[EUR][1000 genomes]
rs1492343	0.83[ASN][1000 genomes]
rs1871847	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590972	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928222	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55874130	0.93[EUR][1000 genomes]
rs55881709	0.89[EUR][1000 genomes]
rs55964918	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140081	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61010376	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800456	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.83[ASN][1000 genomes]
rs73860470	0.86[ASN][1000 genomes]
rs7632345	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635633	0.89[EUR][1000 genomes]
rs7635871	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv822194	chr3:99600260-99604375	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99595200-99602800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:99595400-99602800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:99595400-99603000	Weak transcription	Stomach Mucosa	stomach
4	chr3:99595400-99603400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:99595400-99603400	Weak transcription	Small Intestine	intestine
6	chr3:99595400-99608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:99595600-99602600	Weak transcription	Fetal Intestine Large	intestine
8	chr3:99595600-99603200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:99595600-99607400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:99595600-99612800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:99595800-99603200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:99596000-99603000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:99596000-99603200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:99596600-99614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:99596800-99602600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:99597000-99603400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:99597200-99602800	Weak transcription	K562	blood
18	chr3:99597200-99603000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:99597200-99603400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:99597200-99614200	Weak transcription	HMEC	breast
21	chr3:99597400-99602800	Weak transcription	NHEK	skin
22	chr3:99597800-99603400	Weak transcription	GM12878-XiMat	blood
23	chr3:99600200-99603200	Enhancers	HUVEC	blood vessel
24	chr3:99600600-99602800	Weak transcription	Psoas Muscle	Psoas
25	chr3:99600600-99603400	Weak transcription	Brain Anterior Caudate	brain
26	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
27	chr3:99601400-99603200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:99601600-99603400	Weak transcription	Adipose Nuclei	Adipose
29	chr3:99601800-99603200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:99601800-99604800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:99602000-99604600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:99602000-99605400	Enhancers	HepG2	liver

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