Variant report

Variant	rs3780126
Chromosome Location	chr8:63949912-63949913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:63940680..63942601-chr8:63949219..63951590,2	MCF-7	breast:
2	chr8:62626734..62628934-chr8:63949908..63951935,2	K562	blood:
3	chr8:63925789..63928059-chr8:63949158..63951177,2	MCF-7	breast:
4	chr8:63949699..63952423-chr8:63997523..63999992,2	K562	blood:
5	chr8:62625715..62628343-chr8:63949746..63952148,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198363	Chromatin interaction
ENSG00000137561	Chromatin interaction
ENSG00000264408	Chromatin interaction
ENSG00000137563	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10094071	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10106587	0.80[CEU][hapmap]
rs11995525	0.81[CEU][hapmap]
rs12679179	0.93[ASN][1000 genomes]
rs12682204	0.93[ASN][1000 genomes]
rs13248452	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1350058	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2198689	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2353903	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2736681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28366966	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28429792	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28595528	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28816542	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34099334	0.90[ASN][1000 genomes]
rs4546655	0.89[ASN][1000 genomes]
rs4570149	0.83[AMR][1000 genomes]
rs4606052	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs4739043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4739045	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60941985	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6472067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6472068	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6472071	0.84[EUR][1000 genomes]
rs6472075	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6994076	0.85[CEU][hapmap]
rs6996155	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6996325	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7001383	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7004934	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7005322	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7007125	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7386567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7830578	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7832731	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033527	chr8:63673915-64073735	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3780126	CRH	cis	cerebellum	SCAN
rs3780126	LOC643763	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:63922800-63950000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:63922800-63950000	Weak transcription	HMEC	breast
3	chr8:63922800-63950800	Weak transcription	Fetal Muscle Leg	muscle
4	chr8:63923800-63950600	Weak transcription	Fetal Kidney	kidney
5	chr8:63931400-63950000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:63935800-63950000	Weak transcription	NHDF-Ad	bronchial
7	chr8:63938000-63950000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr8:63938200-63950600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr8:63939200-63950000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:63942600-63950000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr8:63945800-63950600	Weak transcription	Fetal Intestine Small	intestine
12	chr8:63945800-63950800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr8:63946000-63950600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr8:63946000-63950800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr8:63948600-63950000	Enhancers	NH-A	brain
16	chr8:63948600-63950600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr8:63949000-63950000	Flanking Active TSS	Liver	Liver
18	chr8:63949000-63950200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:63949000-63950400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr8:63949000-63950400	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr8:63949000-63950400	Flanking Active TSS	HepG2	liver
22	chr8:63949200-63950200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr8:63949200-63950200	Enhancers	HUVEC	blood vessel
24	chr8:63949200-63950400	Enhancers	Fetal Brain Male	brain
25	chr8:63949200-63950600	Enhancers	NHEK	skin
26	chr8:63949400-63950000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr8:63949400-63950000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr8:63949400-63950400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr8:63949400-63950600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr8:63949400-63951000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr8:63949600-63950200	Flanking Active TSS	K562	blood
32	chr8:63949600-63950400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr8:63949600-63950400	Flanking Active TSS	GM12878-XiMat	blood
34	chr8:63949600-63950800	Weak transcription	Brain Angular Gyrus	brain
35	chr8:63949800-63950000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr8:63949800-63950000	Enhancers	Muscle Satellite Cultured Cells	--
37	chr8:63949800-63950000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:63949800-63950000	Enhancers	Esophagus	oesophagus
39	chr8:63949800-63950000	Enhancers	Fetal Intestine Large	intestine
40	chr8:63949800-63950000	Enhancers	A549	lung
41	chr8:63949800-63950000	Enhancers	Hela-S3	cervix
42	chr8:63949800-63950200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr8:63949800-63950400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr8:63949800-63950400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr8:63949800-63950400	Flanking Active TSS	Fetal Brain Female	brain
46	chr8:63949800-63950800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr8:63949800-63952600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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