Variant report

Variant	rs3821689
Chromosome Location	chr3:53208917-53208918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53187108..53189082-chr3:53208380..53210944,2	MCF-7	breast:
2	chr3:53206928..53209011-chr3:53211960..53213627,2	K562	blood:
3	chr3:53163779..53165542-chr3:53208632..53210403,2	MCF-7	breast:
4	chr3:53189193..53191628-chr3:53207314..53210286,3	MCF-7	breast:
5	chr3:53198720..53200683-chr3:53205526..53209327,4	K562	blood:
6	chr3:53204421..53206931-chr3:53208299..53209885,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11130347	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130350	0.95[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1483185	0.81[JPT][hapmap]
rs1483186	0.81[JPT][hapmap]
rs1872035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2306571	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3773723	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773725	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773726	0.90[JPT][hapmap]
rs3773727	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3773728	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773729	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773733	0.90[JPT][hapmap]
rs3796256	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687571	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6764111	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6778964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750527	0.82[YRI][hapmap]

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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3821689	SLC38A3	cis	cerebellum	SCAN
rs3821689	CAMKV	cis	cerebellum	SCAN
rs3821689	POC1A	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53196400-53210200	Weak transcription	Psoas Muscle	Psoas
2	chr3:53196400-53212400	Weak transcription	Aorta	Aorta
3	chr3:53197200-53213400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
5	chr3:53197800-53214000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:53198000-53215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:53201200-53210400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:53201400-53212400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:53201400-53212600	Weak transcription	Ovary	ovary
11	chr3:53201400-53212800	Weak transcription	Left Ventricle	heart
12	chr3:53201600-53209400	Weak transcription	HSMM	muscle
13	chr3:53201600-53212800	Weak transcription	NHDF-Ad	bronchial
14	chr3:53201600-53228000	Weak transcription	NH-A	brain
15	chr3:53202000-53209400	Weak transcription	Osteobl	bone
16	chr3:53202000-53212400	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:53202000-53212600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:53202000-53228400	Weak transcription	Fetal Kidney	kidney
19	chr3:53202800-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:53203200-53226800	Strong transcription	Fetal Stomach	stomach
21	chr3:53203600-53211400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:53203600-53212800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:53203600-53229800	Weak transcription	A549	lung
24	chr3:53203800-53210600	Genic enhancers	Spleen	Spleen
25	chr3:53204000-53210400	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr3:53204000-53212600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:53204200-53211400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:53204600-53213600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:53205000-53209200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:53205200-53210600	Genic enhancers	Rectal Mucosa Donor 29	rectum
31	chr3:53205400-53210200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:53205600-53209400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:53205600-53209400	Weak transcription	HMEC	breast
34	chr3:53205600-53210400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:53205600-53211400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:53205600-53229800	Weak transcription	Brain Angular Gyrus	brain
37	chr3:53205800-53209400	Weak transcription	Brain Anterior Caudate	brain
38	chr3:53205800-53213800	Weak transcription	Small Intestine	intestine
39	chr3:53206000-53212400	Weak transcription	Fetal Lung	lung
40	chr3:53206000-53212600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:53206000-53213600	Weak transcription	Brain Substantia Nigra	brain
42	chr3:53206000-53213800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:53206000-53219400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:53206200-53209600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:53206200-53210200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:53206200-53211800	Genic enhancers	Adipose Nuclei	Adipose
47	chr3:53206400-53211000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:53206400-53212400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:53206400-53216600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:53206400-53217000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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