Variant report

Variant	rs236473
Chromosome Location	chr6:36692264-36692265
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36648503..36650842-chr6:36690770..36692686,2	MCF-7	breast:
2	chr6:36633980..36636533-chr6:36690989..36693316,2	MCF-7	breast:
3	chr6:36586905..36589063-chr6:36691247..36692772,2	MCF-7	breast:
4	chr6:36571240..36574099-chr6:36691059..36693876,2	K562	blood:
5	chr6:36626473..36628728-chr6:36691772..36694267,2	MCF-7	breast:
6	chr6:36592044..36592560-chr6:36692001..36692530,2	K562	blood:
7	chr6:36689656..36693910-chr6:36696758..36700115,6	K562	blood:
8	chr6:36692117..36693169-chr6:36726597..36727520,3	MCF-7	breast:
9	chr6:36591305..36591878-chr6:36692059..36693073,8	K562	blood:
10	chr6:36581615..36586295-chr6:36690989..36695468,6	MCF-7	breast:
11	chr6:36582741..36583569-chr6:36692167..36692864,2	MCF-7	breast:
12	chr6:36589424..36591252-chr6:36691223..36692725,2	MCF-7	breast:
13	chr6:36655048..36657495-chr6:36690151..36694122,3	MCF-7	breast:
14	chr6:36575353..36578968-chr6:36688808..36692284,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263894	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1065258	0.86[CHB][hapmap]
rs1065259	0.87[CHB][hapmap]
rs1065261	0.87[CHB][hapmap]
rs10947627	0.86[CHB][hapmap]
rs12194367	0.87[CHB][hapmap]
rs129546	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13193217	0.86[CHB][hapmap]
rs236475	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs236476	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs236477	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs236484	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs236486	0.88[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs743870	0.82[CHB][hapmap]
rs7741255	0.87[CHB][hapmap]
rs7763347	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv885809	chr6:36687518-36719079	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs236473	PNPLA1	cis	parietal	SCAN
rs236473	FLJ43093	cis	multi-tissue	Pritchard
rs236473	LHFPL5	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36661400-36696400	Weak transcription	Right Atrium	heart
2	chr6:36671800-36694000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr6:36672200-36693600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:36677000-36694000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:36683800-36695200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:36688200-36692400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:36688400-36692400	Weak transcription	Primary B cells from cord blood	blood
8	chr6:36688400-36702200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:36688600-36692400	Weak transcription	GM12878-XiMat	blood
10	chr6:36689200-36702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:36689800-36693600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:36689800-36696600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:36690000-36692600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:36690000-36692600	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:36690000-36693800	Weak transcription	Fetal Heart	heart
16	chr6:36690400-36696400	Weak transcription	Spleen	Spleen
17	chr6:36690400-36702600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:36690600-36695200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:36690800-36692400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:36690800-36695400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:36691000-36695200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:36691200-36694400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:36691200-36695200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:36691200-36695200	Weak transcription	HMEC	breast
25	chr6:36691200-36695200	Weak transcription	NHEK	skin
26	chr6:36692000-36696600	Enhancers	Primary B cells from peripheral blood	blood

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