Variant report

Variant	rs3786869
Chromosome Location	chr19:38400324-38400325
allele	C/T
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	WRNIP1	chr19:38400136-38400357	GM12878	blood:	n/a	n/a
2	BHLHE40	chr19:38400252-38400772	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:38396652-38400700	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38395556..38401665-chr19:38419693..38425913,12	MCF-7	breast:
2	chr19:38399136..38401318-chr19:38404847..38407238,2	MCF-7	breast:
3	chr19:38393450..38400778-chr19:38419865..38427350,17	MCF-7	breast:

Variant related genes	Relation type
WDR87	TF binding region
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10404159	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10404567	0.87[CEU][hapmap]
rs10415399	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10420746	0.83[CEU][hapmap]
rs11083441	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1119229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12608883	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1291	0.87[CEU][hapmap]
rs12973580	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12974225	0.87[CEU][hapmap]
rs1643460	0.84[EUR][1000 genomes]
rs1643461	0.88[EUR][1000 genomes]
rs1643466	0.82[CEU][hapmap]
rs1643467	0.82[CEU][hapmap]
rs1643468	0.82[CEU][hapmap]
rs1725481	0.83[CEU][hapmap]
rs1725482	0.87[CEU][hapmap]
rs1725499	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2075281	0.83[CEU][hapmap]
rs241932	0.87[CEU][hapmap]
rs28460297	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909098	0.87[CEU][hapmap]
rs2972437	0.87[CEU][hapmap]
rs2972438	0.87[CEU][hapmap]
rs2972439	0.87[CEU][hapmap]
rs353410	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs353411	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs353414	0.82[CEU][hapmap]
rs353415	0.83[CEU][hapmap]
rs353423	0.82[CEU][hapmap]
rs3865514	1.00[YRI][hapmap]
rs4239516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802144	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802147	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802151	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4803524	0.87[CEU][hapmap]
rs4803551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803573	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705491	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705492	0.83[CEU][hapmap]
rs705493	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs705494	0.87[CEU][hapmap]
rs705495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705499	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250409	0.87[CEU][hapmap]
rs8102579	0.87[CEU][hapmap]
rs8108434	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109053	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109835	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110284	0.83[CEU][hapmap]
rs8112706	0.83[CEU][hapmap]
rs8113273	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8113521	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs833895	0.82[CEU][hapmap]
rs833926	0.83[CEU][hapmap]
rs856300	0.81[CEU][hapmap]
rs856304	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1064401	chr19:38387797-38427984	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3786869	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38396400-38400600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:38397000-38401000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr19:38398600-38422600	Weak transcription	Aorta	Aorta
4	chr19:38398800-38400400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr19:38398800-38400400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr19:38398800-38400400	Enhancers	Fetal Muscle Trunk	muscle
7	chr19:38398800-38400400	Enhancers	Fetal Thymus	thymus
8	chr19:38398800-38400400	Enhancers	Pancreas	Pancrea
9	chr19:38398800-38400600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr19:38398800-38405200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:38398800-38433800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:38399000-38400400	Enhancers	H9 Cell Line	embryonic stem cell
13	chr19:38399000-38400400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:38399000-38400600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:38399000-38400800	Enhancers	HepG2	liver
16	chr19:38399000-38401200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr19:38399000-38418400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr19:38399000-38422400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:38399200-38400400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:38399200-38400400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:38399200-38400400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:38399200-38400600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:38399200-38400600	Enhancers	HSMMtube	muscle
24	chr19:38399200-38400600	Enhancers	HUVEC	blood vessel
25	chr19:38399200-38400800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr19:38399200-38401000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr19:38399200-38401200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr19:38399200-38401200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:38399200-38401400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr19:38399200-38401400	Weak transcription	HMEC	breast
31	chr19:38399200-38401800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:38399200-38402800	Weak transcription	Fetal Intestine Small	intestine
33	chr19:38399200-38404800	Weak transcription	Primary T cells from cord blood	blood
34	chr19:38399200-38405000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr19:38399200-38405400	Weak transcription	Adipose Nuclei	Adipose
36	chr19:38399200-38405400	Weak transcription	Fetal Muscle Leg	muscle
37	chr19:38399200-38405400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:38399200-38409400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr19:38399200-38411000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:38399200-38411000	Weak transcription	Stomach Mucosa	stomach
41	chr19:38399200-38411400	Weak transcription	NHEK	skin
42	chr19:38399200-38411800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:38399200-38411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:38399200-38415600	Weak transcription	Hela-S3	cervix
45	chr19:38399200-38416000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:38399200-38422400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:38399200-38422600	Weak transcription	Fetal Lung	lung
48	chr19:38399200-38424600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:38399400-38400400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:38399400-38400600	Flanking Active TSS	GM12878-XiMat	blood

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