Variant report

Variant	rs1928565
Chromosome Location	chr3:67580121-67580122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:67579980-67580130	HBMEC	blood vessel:	n/a	n/a
2	E2F4	chr3:67580083-67580283	MCF10A-Er-Src	breast:	n/a	n/a
3	RAD21	chr3:67579781-67580187	A549	lung:	n/a	n/a
4	RAD21	chr3:67579892-67580164	HepG2	liver:	n/a	n/a
5	RAD21	chr3:67579830-67580121	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr3:67579779-67580219	HepG2	liver:	n/a	n/a
7	CTCF	chr3:67579920-67580210	NHDF-neo	bronchial:	n/a	n/a
8	RAD21	chr3:67579709-67580217	MCF-7	breast:	n/a	n/a
9	CTCF	chr3:67579835-67580131	GM12878	blood:	n/a	n/a
10	RAD21	chr3:67579741-67580159	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr3:67579760-67580142	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:67579848-67580146	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67579489..67580411-chr3:67840544..67841101,2	MCF-7	breast:

Variant related genes	Relation type
SUCLG2	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1122766	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1590874	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1928550	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2634723	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2634732	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2634736	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634738	0.82[AMR][1000 genomes]
rs2634742	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634743	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2634744	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2772447	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2772448	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2772449	0.82[AMR][1000 genomes]
rs2772450	0.84[AMR][1000 genomes]
rs2772451	0.84[AMR][1000 genomes]
rs2772469	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2772471	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4856788	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9818350	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1928565	C3orf64	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67521600-67580400	Weak transcription	Stomach Mucosa	stomach
2	chr3:67526800-67583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:67541400-67582000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:67544200-67580200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:67557400-67583200	Weak transcription	K562	blood
6	chr3:67558400-67580200	Weak transcription	Fetal Thymus	thymus
7	chr3:67560200-67581800	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:67560600-67580200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:67560600-67586200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:67560600-67620800	Weak transcription	Esophagus	oesophagus
11	chr3:67563800-67580800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:67564800-67580400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:67565000-67580200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:67565600-67595800	Weak transcription	Fetal Kidney	kidney
15	chr3:67566600-67581000	Weak transcription	Gastric	stomach
16	chr3:67566800-67580200	Weak transcription	HUVEC	blood vessel
17	chr3:67566800-67581800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:67566800-67582000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:67567000-67581200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:67567000-67581800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:67567200-67581400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:67568000-67580600	Weak transcription	Colonic Mucosa	Colon
23	chr3:67568000-67590600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:67568600-67580400	Weak transcription	Placenta	Placenta
25	chr3:67572800-67581600	Strong transcription	Primary B cells from cord blood	blood
26	chr3:67576200-67585400	Enhancers	NHDF-Ad	bronchial
27	chr3:67576800-67580600	Strong transcription	Primary T cells from cord blood	blood
28	chr3:67577200-67580400	Weak transcription	NHEK	skin
29	chr3:67577200-67581000	Weak transcription	HMEC	breast
30	chr3:67577400-67580200	Weak transcription	HSMMtube	muscle
31	chr3:67577400-67581800	Weak transcription	NH-A	brain
32	chr3:67578000-67580200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:67578000-67581400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:67578200-67580800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr3:67578200-67581200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:67578200-67581800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:67578200-67585600	Weak transcription	Psoas Muscle	Psoas
38	chr3:67578200-67600400	Weak transcription	Lung	lung
39	chr3:67578200-67612400	Weak transcription	Spleen	Spleen
40	chr3:67578200-67634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:67578400-67580200	Weak transcription	Thymus	Thymus
42	chr3:67578400-67583800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:67578400-67593800	Weak transcription	Fetal Intestine Small	intestine
44	chr3:67578600-67581000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:67578600-67581800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:67578600-67582200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:67578600-67601800	Weak transcription	Left Ventricle	heart
48	chr3:67578800-67580600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:67579000-67580400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:67579000-67581000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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