Variant report

Variant	rs9380007
Chromosome Location	chr6:27660508-27660509
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27658926..27663446-chr6:27685398..27690588,6	K562	blood:
2	chr6:27651170..27656145-chr6:27660253..27663653,4	MCF-7	breast:
3	chr6:27260766..27263711-chr6:27659606..27661608,2	K562	blood:
4	chr6:27638340..27640249-chr6:27659440..27661461,2	K562	blood:
5	chr6:27659790..27663314-chr6:27665578..27668905,6	K562	blood:
6	chr6:27653789..27659338-chr6:27659392..27663401,13	K562	blood:
7	chr6:27651230..27653525-chr6:27660393..27663354,2	MCF-7	breast:
8	chr6:27659151..27662876-chr6:27687364..27691190,4	K562	blood:
9	chr6:27660493..27662208-chr6:27687324..27689056,2	MCF-7	breast:
10	chr6:27517580..27520296-chr6:27658437..27660745,2	K562	blood:
11	chr6:26595641..26598321-chr6:27660238..27661908,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000146109	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1022486	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs10946935	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs10946938	0.93[CHD][hapmap];0.91[JPT][hapmap]
rs10946940	0.88[CHD][hapmap];0.91[JPT][hapmap]
rs200480	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap]
rs2056924	0.81[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2179096	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2294480	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2294481	0.91[JPT][hapmap]
rs4713112	0.86[JPT][hapmap]
rs4713120	0.85[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57252182	0.86[EUR][1000 genomes]
rs6456799	0.86[CHD][hapmap];0.91[JPT][hapmap]
rs6899903	0.81[ASN][1000 genomes]
rs6915266	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs6915987	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.80[TSI][hapmap]
rs6916878	0.83[JPT][hapmap]
rs6921256	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs6934437	0.86[JPT][hapmap]
rs6934794	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs7764081	0.86[JPT][hapmap]
rs9295747	0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs9348772	0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9366697	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9368527	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393830	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9393831	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs9468209	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468213	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv883511	chr6:27623511-27660508	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv518945	chr6:27634640-27668013	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv437481	chr6:27655096-27683572	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv601204	chr6:27655564-27689502	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1023808	chr6:27656049-27674354	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9380007	ZNF323	cis	cerebellum	SCAN
rs9380007	ZNF323	cis	parietal	SCAN
rs9380007	ZSCAN16	cis	parietal	SCAN
rs9380007	AL022393.7	cis	Muscle Skeletal	GTEx
rs9380007	HIST1H3I	cis	cerebellum	SCAN
rs9380007	NKAPL	cis	parietal	SCAN
rs9380007	ZKSCAN3	cis	cerebellum	SCAN
rs9380007	ZKSCAN3	cis	parietal	SCAN
rs9380007	ZSCAN23	cis	cerebellum	SCAN
rs9380007	ABT1	cis	cerebellum	SCAN
rs9380007	BTN3A3	cis	parietal	SCAN
rs9380007	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27655800-27661400	Weak transcription	Lung	lung
2	chr6:27656200-27661000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:27656200-27661600	Weak transcription	Adipose Nuclei	Adipose
4	chr6:27656200-27661600	Weak transcription	Right Atrium	heart
5	chr6:27656400-27660800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:27656400-27661000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:27656400-27661200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:27656400-27661200	Weak transcription	HMEC	breast
9	chr6:27656400-27661400	Weak transcription	Pancreas	Pancrea
10	chr6:27656600-27661400	Weak transcription	Dnd41	blood
11	chr6:27657000-27661000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:27657200-27661000	Weak transcription	K562	blood
13	chr6:27657200-27661200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:27657400-27661000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:27657600-27661000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:27658600-27661200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:27658800-27661200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:27659000-27661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:27659000-27661400	Weak transcription	NHEK	skin
20	chr6:27659400-27661000	Weak transcription	HepG2	liver
21	chr6:27659600-27661200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:27660200-27661000	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links