Variant report

Variant	rs3821564
Chromosome Location	chr3:69154386-69154387
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69133410..69135545-chr3:69153469..69155748,2	MCF-7	breast:
2	chr3:69153444..69155316-chr3:69160247..69161792,2	MCF-7	breast:
3	chr3:69134734..69136493-chr3:69152405..69154710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144746	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10489	0.80[ASN][1000 genomes]
rs1051901	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131960	1.00[EUR][1000 genomes]
rs12054346	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17005366	1.00[EUR][1000 genomes]
rs3772980	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772983	1.00[EUR][1000 genomes]
rs3796213	1.00[ASN][1000 genomes]
rs3796214	1.00[EUR][1000 genomes]
rs56152276	1.00[EUR][1000 genomes]
rs56194306	1.00[EUR][1000 genomes]
rs56280964	1.00[EUR][1000 genomes]
rs57159802	1.00[EUR][1000 genomes]
rs58277851	1.00[EUR][1000 genomes]
rs59090383	1.00[EUR][1000 genomes]
rs60230066	0.97[ASN][1000 genomes]
rs60474520	1.00[EUR][1000 genomes]
rs72924853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835722	1.00[EUR][1000 genomes]
rs73835726	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73835727	1.00[EUR][1000 genomes]
rs73835728	1.00[EUR][1000 genomes]
rs73835729	1.00[EUR][1000 genomes]
rs7617775	0.86[EUR][1000 genomes]
rs7621394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621929	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625579	0.80[ASN][1000 genomes]
rs7627893	0.80[ASN][1000 genomes]
rs7629932	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3821564	ENSG00000144746	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69135200-69155200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:69135800-69155800	Weak transcription	Fetal Kidney	kidney
3	chr3:69136800-69156400	Weak transcription	Fetal Brain Male	brain
4	chr3:69139800-69154600	Weak transcription	A549	lung
5	chr3:69142000-69160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:69143600-69160200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:69145600-69160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:69145800-69160200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:69146200-69160200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:69147400-69160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:69148600-69155200	Strong transcription	Primary B cells from cord blood	blood
12	chr3:69148600-69155800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:69148800-69155600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:69148800-69155600	Strong transcription	GM12878-XiMat	blood
15	chr3:69148800-69155800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr3:69148800-69155800	Strong transcription	Dnd41	blood
17	chr3:69149000-69154800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:69149200-69155400	Strong transcription	Fetal Thymus	thymus
19	chr3:69150000-69155400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr3:69150200-69154800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:69150200-69155400	Strong transcription	NH-A	brain
22	chr3:69150400-69155800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:69150600-69154400	Strong transcription	Adipose Nuclei	Adipose
24	chr3:69150600-69155600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:69150600-69155800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr3:69150800-69154400	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:69150800-69154400	Strong transcription	Fetal Lung	lung
28	chr3:69150800-69155600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:69150800-69155800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:69150800-69155800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:69151000-69154600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:69151000-69155400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:69151000-69155400	Strong transcription	Liver	Liver
34	chr3:69151000-69155600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:69151000-69155800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:69151200-69154600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:69151200-69157800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:69151800-69154600	Weak transcription	Hela-S3	cervix
39	chr3:69151800-69155400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:69151800-69155600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:69151800-69155600	Weak transcription	Fetal Stomach	stomach
42	chr3:69151800-69155800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:69151800-69155800	Weak transcription	HepG2	liver
44	chr3:69151800-69156400	Weak transcription	Fetal Intestine Small	intestine
45	chr3:69152000-69155400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:69152000-69157000	Weak transcription	Stomach Mucosa	stomach
47	chr3:69152000-69160200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:69152400-69155400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr3:69152800-69155200	Strong transcription	Brain Germinal Matrix	brain
50	chr3:69152800-69157000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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