Variant report

Variant	rs3804288
Chromosome Location	chr6:146868048-146868049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:146836468..146839351-chr6:146867182..146869827,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11155475	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs12189826	0.81[EUR][1000 genomes]
rs3804286	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3804289	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570768	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6915731	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs6915941	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6918907	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6939108	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7773384	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9373498	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377003	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs9377004	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs9399580	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033913	chr6:146572989-147092365	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538466	chr6:146572989-147092365	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv886749	chr6:146679735-147123699	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3804288	STX11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146864000-146868400	Active TSS	Right Atrium	heart
2	chr6:146864000-146868800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:146864200-146868600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:146864200-146870600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:146864400-146868400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:146865000-146868200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr6:146865000-146868200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:146865400-146868800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:146865800-146869600	Weak transcription	Spleen	Spleen
10	chr6:146865800-146877400	Weak transcription	Placenta	Placenta
11	chr6:146865800-146878200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:146866000-146868400	Flanking Active TSS	HUVEC	blood vessel
13	chr6:146866000-146870600	Weak transcription	Ovary	ovary
14	chr6:146866200-146868400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:146866200-146868800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:146866400-146869000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr6:146866400-146881800	Weak transcription	Brain Germinal Matrix	brain
18	chr6:146866600-146868400	Active TSS	Stomach Smooth Muscle	stomach
19	chr6:146866600-146869600	Weak transcription	K562	blood
20	chr6:146866600-146870600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:146866600-146870600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:146866600-146870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:146866600-146871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:146866600-146875800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:146866600-146876200	Weak transcription	Psoas Muscle	Psoas
26	chr6:146866600-146877800	Weak transcription	Gastric	stomach
27	chr6:146866600-146877800	Weak transcription	Lung	lung
28	chr6:146866600-146883800	Weak transcription	Small Intestine	intestine
29	chr6:146866600-146885800	Weak transcription	Pancreas	Pancrea
30	chr6:146866800-146868200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:146866800-146868400	Enhancers	Fetal Heart	heart
32	chr6:146866800-146870600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:146866800-146877600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:146866800-146878000	Weak transcription	Brain Substantia Nigra	brain
35	chr6:146867000-146868200	Enhancers	Fetal Lung	lung
36	chr6:146867000-146868200	Active TSS	Fetal Muscle Leg	muscle
37	chr6:146867000-146868600	Enhancers	Liver	Liver
38	chr6:146867000-146870000	Enhancers	Colon Smooth Muscle	Colon
39	chr6:146867000-146872400	Weak transcription	Left Ventricle	heart
40	chr6:146867000-146876000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:146867000-146877200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:146867000-146877800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:146867000-146880600	Weak transcription	Right Ventricle	heart
44	chr6:146867200-146868200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:146867200-146868400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr6:146867200-146868800	Enhancers	HepG2	liver
47	chr6:146867200-146869400	Enhancers	Rectal Smooth Muscle	rectum
48	chr6:146867200-146870600	Weak transcription	Thymus	Thymus
49	chr6:146867200-146870800	Weak transcription	Fetal Kidney	kidney
50	chr6:146867200-146870800	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links