Variant report

Variant	rs6913134
Chromosome Location	chr6:144020391-144020392
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144018054..144020954-chr6:144022528..144024554,3	MCF-7	breast:
2	chr6:143831227..143833944-chr6:144017748..144020555,2	MCF-7	breast:
3	chr6:144020099..144020600-chr6:144334156..144334754,2	K562	blood:
4	chr6:144011387..144013559-chr6:144018568..144021455,2	MCF-7	breast:
5	chr6:144019071..144021984-chr6:144030527..144032678,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000001036	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10872562	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1108314	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11155315	0.81[CHB][hapmap]
rs11155317	0.87[ASN][1000 genomes]
rs12195195	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12198291	0.85[ASN][1000 genomes]
rs12201496	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12206069	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12207002	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.85[ASN][1000 genomes]
rs12208927	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.87[ASN][1000 genomes]
rs12528456	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3924969	0.85[ASN][1000 genomes]
rs6901659	0.94[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs6907410	0.87[ASN][1000 genomes]
rs6915784	0.84[ASN][1000 genomes]
rs7740709	0.89[CHB][hapmap];0.90[ASN][1000 genomes]
rs7741424	0.85[ASN][1000 genomes]
rs7748882	0.81[CHB][hapmap]
rs7766510	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7772565	0.81[CHB][hapmap]
rs8180640	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9373396	0.86[ASN][1000 genomes]
rs9373397	0.81[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9376776	0.85[ASN][1000 genomes]
rs9386042	0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9386043	0.81[CHB][hapmap];0.80[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9390126	0.83[ASN][1000 genomes]
rs9399458	0.90[ASN][1000 genomes]
rs9403521	0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.86[ASN][1000 genomes]
rs9403523	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9496739	0.87[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv886737	chr6:144010570-144033992	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6913134	PLAGL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144005000-144020400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:144011600-144053200	Weak transcription	Hela-S3	cervix
3	chr6:144012200-144026800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:144014200-144027800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:144014200-144039800	Weak transcription	Pancreas	Pancrea
6	chr6:144014400-144022600	Weak transcription	Fetal Intestine Large	intestine
7	chr6:144014800-144020800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:144015400-144020800	Weak transcription	Lung	lung
9	chr6:144015400-144034600	Weak transcription	Esophagus	oesophagus
10	chr6:144015800-144021800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:144016000-144021800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:144016000-144022000	Weak transcription	HSMMtube	muscle
13	chr6:144016200-144021600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:144016200-144023000	Enhancers	Adipose Nuclei	Adipose
15	chr6:144016200-144037200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:144016200-144038000	Weak transcription	NHEK	skin
17	chr6:144016400-144022000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:144016600-144034000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:144016600-144034000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:144016800-144021800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:144017000-144021000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:144017000-144022000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:144017000-144022200	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:144017000-144023000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:144017000-144023200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:144017000-144026800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:144017000-144038200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:144017200-144044200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:144017400-144021600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:144017400-144021800	Weak transcription	Small Intestine	intestine
31	chr6:144017400-144034400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:144017600-144020400	Weak transcription	Psoas Muscle	Psoas
33	chr6:144017600-144026800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:144017800-144020400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr6:144017800-144047200	Weak transcription	K562	blood
36	chr6:144018000-144022200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:144018000-144030800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:144018200-144021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:144018200-144021800	Weak transcription	NHLF	lung
40	chr6:144018200-144022000	Weak transcription	Fetal Heart	heart
41	chr6:144018200-144023000	Weak transcription	Aorta	Aorta
42	chr6:144018200-144026800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:144018200-144044400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:144018400-144020400	Weak transcription	Fetal Lung	lung
45	chr6:144018600-144021800	Weak transcription	Stomach Mucosa	stomach
46	chr6:144018600-144030600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr6:144018800-144020600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:144018800-144020600	Weak transcription	Fetal Kidney	kidney
49	chr6:144019000-144020400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:144019000-144021800	Weak transcription	NH-A	brain

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