Variant report

Variant	rs3773729
Chromosome Location	chr3:53204845-53204846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53195432..53198027-chr3:53202320..53205613,4	K562	blood:
2	chr3:53204421..53206931-chr3:53208299..53209885,2	MCF-7	breast:
3	chr3:53204795..53206722-chr3:53230021..53232845,2	K562	blood:
4	chr3:53199183..53202732-chr3:53204136..53207026,5	K562	blood:

Variant related genes	Relation type
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11130344	0.88[CHD][hapmap]
rs11130345	0.84[CHD][hapmap]
rs11130347	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130350	0.95[CEU][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13085294	0.84[CHD][hapmap]
rs1483185	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs1483186	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1872035	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306571	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2358617	0.84[CHD][hapmap]
rs3773723	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773725	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773726	0.90[JPT][hapmap]
rs3773727	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3773728	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773733	0.90[JPT][hapmap]
rs3796256	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821689	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]
rs4687571	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687706	0.82[ASN][1000 genomes]
rs6778939	0.84[ASN][1000 genomes]
rs6778964	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3773729	SLC38A3	cis	cerebellum	SCAN
rs3773729	CAMKV	cis	cerebellum	SCAN

Chromatin state (count:119 , 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	chr3:53197200-53205400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:53197200-53213400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:53197400-53207000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:53197600-53206600	Genic enhancers	Fetal Intestine Small	intestine
7	chr3:53197600-53206800	Weak transcription	Primary T cells from cord blood	blood
8	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
9	chr3:53197800-53214000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:53198000-53206800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:53198000-53215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:53199600-53205000	Genic enhancers	Esophagus	oesophagus
13	chr3:53200200-53205800	Enhancers	Fetal Muscle Leg	muscle
14	chr3:53200200-53206400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:53200200-53207200	Enhancers	Fetal Thymus	thymus
16	chr3:53200400-53205000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:53200400-53206200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:53200600-53206200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:53200600-53206200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:53200600-53206400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:53200600-53206800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:53200800-53205000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr3:53200800-53206000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:53200800-53207200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr3:53201000-53206000	Weak transcription	Fetal Heart	heart
27	chr3:53201000-53206000	Enhancers	Pancreas	Pancrea
28	chr3:53201000-53206600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:53201000-53207000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:53201200-53205200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:53201200-53210400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:53201400-53212400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:53201400-53212600	Weak transcription	Ovary	ovary
34	chr3:53201400-53212800	Weak transcription	Left Ventricle	heart
35	chr3:53201600-53206200	Weak transcription	NHLF	lung
36	chr3:53201600-53206400	Enhancers	Fetal Intestine Large	intestine
37	chr3:53201600-53209400	Weak transcription	HSMM	muscle
38	chr3:53201600-53212800	Weak transcription	NHDF-Ad	bronchial
39	chr3:53201600-53228000	Weak transcription	NH-A	brain
40	chr3:53202000-53207800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:53202000-53209400	Weak transcription	Osteobl	bone
42	chr3:53202000-53212400	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:53202000-53212600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:53202000-53228400	Weak transcription	Fetal Kidney	kidney
45	chr3:53202400-53205000	Flanking Active TSS	HepG2	liver
46	chr3:53202400-53208400	Weak transcription	NHEK	skin
47	chr3:53202600-53205400	Weak transcription	Fetal Lung	lung
48	chr3:53202600-53205600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:53202800-53205200	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:53202800-53206400	Weak transcription	Right Atrium	heart

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