Variant report

Variant	rs9470449
Chromosome Location	chr6:36947386-36947387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:36947153-36947409	LNCaP	prostate:	n/a	n/a
2	RAD21	chr6:36947047-36947602	MCF-7	breast:	n/a	n/a
3	CTCF	chr6:36947240-36947390	HRPEpiC	eye:	n/a	n/a
4	CTCF	chr6:36947179-36947405	LNCaP	prostate:	n/a	n/a
5	CTCF	chr6:36947190-36947400	GM13977	blood:	n/a	n/a
6	CTCF	chr6:36947002-36947661	A549	lung:	n/a	n/a
7	CTCF	chr6:36947240-36947390	HepG2	liver:	n/a	n/a
8	CTCF	chr6:36947164-36947410	Spleen_OC	spleen:	n/a	n/a
9	RAD21	chr6:36946770-36947609	SK-N-SH	brain:	n/a	chr6:36946961-36946980
10	RAD21	chr6:36947069-36947500	A549	lung:	n/a	n/a
11	CTCF	chr6:36947185-36947390	MCF-7	breast:	n/a	n/a
12	RAD21	chr6:36947167-36947457	MCF-7	breast:	n/a	n/a
13	CTCF	chr6:36947175-36947393	ProgFib	skin:	n/a	n/a
14	CTCF	chr6:36947240-36947390	HEEpiC	esophagus:	n/a	n/a
15	CTCF	chr6:36947240-36947390	GM12869	blood:	n/a	n/a
16	CTCF	chr6:36947177-36947393	GM19239	blood:	n/a	n/a
17	RAD21	chr6:36947102-36947456	IMR90	lung:	n/a	n/a
18	POLR2A	chr6:36947112-36947482	GM12891	blood:	n/a	n/a
19	CTCF	chr6:36947240-36947390	SK-N-SH_RA	brain:	n/a	n/a
20	CTCF	chr6:36947187-36947389	MCF-7	breast:	n/a	n/a
21	CTCF	chr6:36947180-36947391	A549	lung:	n/a	n/a
22	CTCF	chr6:36947078-36947436	A549	lung:	n/a	n/a
23	POLR2A	chr6:36946683-36950240	GM12878	blood:	n/a	n/a
24	SMC3	chr6:36947006-36947607	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr6:36947157-36947410	NHEK	skin:	n/a	n/a
26	RAD21	chr6:36947147-36947457	HepG2	liver:	n/a	n/a
27	CTCF	chr6:36947236-36947405	GM12878	blood:	n/a	n/a
28	RAD21	chr6:36947114-36947493	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr6:36947193-36947386	GM12892	blood:	n/a	n/a
30	CTCF	chr6:36947182-36947388	MCF-7	breast:	n/a	n/a
31	CTCF	chr6:36947174-36947401	Fibrobl	skin:	n/a	n/a
32	RAD21	chr6:36947051-36947592	HCT-116	colon:	n/a	n/a
33	CTCF	chr6:36947193-36947394	MCF-7	breast:	n/a	n/a
34	CTCF	chr6:36947150-36947415	Pancreas_OC	pancreas:	n/a	n/a
35	CTCF	chr6:36946788-36947717	SK-N-SH	brain:	n/a	chr6:36946965-36946975 chr6:36947699-36947712 chr6:36946960-36946978
36	POLR2A	chr6:36947162-36947560	K562	blood:	n/a	n/a
37	CTCF	chr6:36947129-36947428	T-47D	breast:	n/a	n/a
38	CTCF	chr6:36947020-36947418	MCF-7	breast:	n/a	n/a
39	CTCF	chr6:36947203-36947425	GM10266	blood:	n/a	n/a
40	CTCF	chr6:36947091-36947463	A549	lung:	n/a	n/a
41	CTCF	chr6:36947186-36947397	Kidney_OC	kidney:	n/a	n/a
42	RAD21	chr6:36947103-36947406	Hela-S3	cervix:	n/a	n/a
43	CTCF	chr6:36947073-36947523	MCF-7	breast:	n/a	n/a
44	CTCF	chr6:36947240-36947390	HMEC	breast:	n/a	n/a
45	POLR2A	chr6:36946687-36947431	GM12878	blood:	n/a	n/a
46	CTCF	chr6:36947177-36947388	K562	blood:	n/a	n/a
47	CTCF	chr6:36947240-36947390	RPTEC	kidney:	n/a	n/a
48	CTCF	chr6:36947260-36947410	RPTEC	kidney:	n/a	n/a
49	CTCF	chr6:36947240-36947390	HA-sp	spinal cord:	n/a	n/a
50	CTCF	chr6:36947186-36947415	Lung_OC	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36937337..36939324-chr6:36946513..36949209,3	MCF-7	breast:
2	chr6:36937337..36939387-chr6:36947202..36951298,3	MCF-7	breast:
3	chr6:36925903..36928788-chr6:36946034..36948612,2	MCF-7	breast:
4	chr6:36881755..36882648-chr6:36946922..36947744,2	MCF-7	breast:
5	chr6:36947258..36950041-chr6:36986048..36987573,2	MCF-7	breast:
6	chr6:36859467..36861214-chr6:36946657..36948783,2	MCF-7	breast:

No data

Variant related genes	Relation type
MTCH1	TF binding region
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10498737	1.00[CHB][hapmap]
rs10947658	1.00[CHB][hapmap]
rs11961047	1.00[CHB][hapmap]
rs11969088	0.96[EUR][1000 genomes]
rs12210148	1.00[CHB][hapmap]
rs13193599	1.00[CHB][hapmap]
rs13193613	1.00[CHB][hapmap]
rs16889199	1.00[CHB][hapmap]
rs16889344	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs16889347	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs16889349	0.85[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs2395668	1.00[CHB][hapmap]
rs61748598	0.96[EUR][1000 genomes]
rs6915283	1.00[CHB][hapmap]
rs6919096	1.00[CHB][hapmap]
rs6938178	1.00[CHB][hapmap]
rs733461	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296205	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs943834	0.86[GIH][hapmap]
rs9470448	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470493	1.00[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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	esv988069	chr6:36942299-36951067	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9470449	PI16	cis	cerebellum	SCAN
rs9470449	SRSF3	cis	parietal	SCAN
rs9470449	ZFAND3	cis	parietal	SCAN
rs9470449	CDKN1A	cis	cerebellum	SCAN
rs9470449	PI16	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36931800-36948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:36932800-36947400	Strong transcription	Fetal Stomach	stomach
4	chr6:36934000-36949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr6:36934000-36951600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:36934200-36947400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:36934200-36949200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:36934200-36950400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:36934400-36947400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr6:36934400-36947800	Strong transcription	Dnd41	blood
11	chr6:36934400-36949200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:36934600-36947400	Strong transcription	NH-A	brain
13	chr6:36934600-36947600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr6:36934600-36949200	Strong transcription	Placenta	Placenta
15	chr6:36934800-36949600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:36935000-36947400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:36935000-36947400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:36935000-36947400	Strong transcription	HepG2	liver
19	chr6:36935000-36947600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:36935000-36948000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:36935000-36948400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:36935000-36949800	Genic enhancers	Left Ventricle	heart
23	chr6:36935000-36950200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr6:36935200-36947400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:36935200-36948200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:36935200-36948600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:36935400-36947400	Strong transcription	Spleen	Spleen
28	chr6:36935400-36948400	Strong transcription	GM12878-XiMat	blood
29	chr6:36936200-36949000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr6:36938600-36948400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:36939000-36951200	Strong transcription	HSMM	muscle
32	chr6:36939400-36949600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:36939600-36947800	Strong transcription	Lung	lung
34	chr6:36939600-36948800	Strong transcription	NHEK	skin
35	chr6:36939600-36950600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:36940200-36947800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:36940800-36948600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:36941200-36950600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:36942800-36948800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr6:36943600-36948400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:36944000-36949400	Genic enhancers	Right Ventricle	heart
42	chr6:36945000-36948600	Strong transcription	K562	blood
43	chr6:36945000-36949200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:36945000-36951200	Enhancers	Fetal Heart	heart
45	chr6:36945200-36948600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:36945400-36951400	Weak transcription	Fetal Kidney	kidney
47	chr6:36945600-36948600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:36945600-36949400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:36945600-36949800	Genic enhancers	Stomach Smooth Muscle	stomach
50	chr6:36946000-36948000	Weak transcription	Primary B cells from cord blood	blood

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