Variant report

Variant	rs3804286
Chromosome Location	chr6:146869009-146869010
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146863064..146866628-chr6:146868587..146870728,3	K562	blood:
2	chr6:146863630..146867069-chr6:146868251..146871373,4	MCF-7	breast:
3	chr6:146836468..146839351-chr6:146867182..146869827,2	K562	blood:

Variant related genes	Relation type
ENSG00000118508	Chromatin interaction

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];0.84[TSI][hapmap];0.94[EUR][1000 genomes]
rs12189826	0.94[EUR][1000 genomes]
rs3804288	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	0.90[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]
rs6570768	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6915731	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs6918907	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6939108	0.91[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs7773384	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373498	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377003	0.95[CEU][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs9377004	0.95[CEU][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9390393	0.91[EUR][1000 genomes]
rs9399580	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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
rs3804286	STX11	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146864200-146870600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:146865800-146869600	Weak transcription	Spleen	Spleen
3	chr6:146865800-146877400	Weak transcription	Placenta	Placenta
4	chr6:146865800-146878200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:146866000-146870600	Weak transcription	Ovary	ovary
6	chr6:146866400-146881800	Weak transcription	Brain Germinal Matrix	brain
7	chr6:146866600-146869600	Weak transcription	K562	blood
8	chr6:146866600-146870600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:146866600-146870600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:146866600-146870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:146866600-146871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:146866600-146875800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:146866600-146876200	Weak transcription	Psoas Muscle	Psoas
14	chr6:146866600-146877800	Weak transcription	Gastric	stomach
15	chr6:146866600-146877800	Weak transcription	Lung	lung
16	chr6:146866600-146883800	Weak transcription	Small Intestine	intestine
17	chr6:146866600-146885800	Weak transcription	Pancreas	Pancrea
18	chr6:146866800-146870600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:146866800-146877600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:146866800-146878000	Weak transcription	Brain Substantia Nigra	brain
21	chr6:146867000-146870000	Enhancers	Colon Smooth Muscle	Colon
22	chr6:146867000-146872400	Weak transcription	Left Ventricle	heart
23	chr6:146867000-146876000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:146867000-146877200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:146867000-146877800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:146867000-146880600	Weak transcription	Right Ventricle	heart
27	chr6:146867200-146869400	Enhancers	Rectal Smooth Muscle	rectum
28	chr6:146867200-146870600	Weak transcription	Thymus	Thymus
29	chr6:146867200-146870800	Weak transcription	Fetal Kidney	kidney
30	chr6:146867200-146870800	Weak transcription	Fetal Thymus	thymus
31	chr6:146867200-146871400	Weak transcription	Fetal Stomach	stomach
32	chr6:146867200-146871600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:146867200-146875600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:146867200-146875600	Weak transcription	Colonic Mucosa	Colon
35	chr6:146867200-146877800	Weak transcription	Primary T cells from cord blood	blood
36	chr6:146867400-146870600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr6:146867400-146870600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr6:146867400-146875400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:146867400-146875800	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:146867400-146877400	Weak transcription	Fetal Intestine Small	intestine
41	chr6:146867600-146870600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:146867800-146870600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:146867800-146870800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:146867800-146875200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr6:146868000-146870600	Weak transcription	Fetal Intestine Large	intestine
46	chr6:146868000-146873800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:146868200-146869800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:146868200-146870000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:146868200-146870000	Weak transcription	Aorta	Aorta
50	chr6:146868200-146870400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links