Variant report

Variant	rs6478563
Chromosome Location	chr9:100864919-100864920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100864402..100866260-chr9:100880228..100882375,2	K562	blood:
2	chr9:100862346..100865171-chr9:100880500..100883017,2	K562	blood:
3	chr9:100860198..100865318-chr9:100878989..100883996,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10985048	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10985065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12552242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16912622	0.82[JPT][hapmap]
rs2281732	0.82[JPT][hapmap]
rs4742716	0.82[JPT][hapmap]
rs4743157	0.82[JPT][hapmap]
rs4743158	0.82[JPT][hapmap]
rs4743164	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55972150	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478539	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs6478556	0.82[JPT][hapmap]
rs7022455	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7852752	0.83[CEU][hapmap]
rs7855251	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7865340	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7869762	0.82[JPT][hapmap]

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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040483	chr9:100835325-100868437	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv614935	chr9:100861387-100876284	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6478563	ZNF169	cis	cerebellum	SCAN
rs6478563	C9orf156	cis	parietal	SCAN
rs6478563	NANS	cis	parietal	SCAN
rs6478563	PHF2	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100847400-100869400	Weak transcription	A549	lung
2	chr9:100847600-100867000	Weak transcription	Hela-S3	cervix
3	chr9:100850400-100868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:100850400-100880400	Weak transcription	HSMM	muscle
5	chr9:100850600-100875400	Weak transcription	NHLF	lung
6	chr9:100850600-100880600	Weak transcription	Fetal Lung	lung
7	chr9:100854600-100870800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:100854800-100870800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:100855000-100866800	Weak transcription	Placenta	Placenta
10	chr9:100855000-100868200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:100857800-100869400	Weak transcription	Left Ventricle	heart
12	chr9:100858200-100868000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:100858200-100869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:100858400-100872000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:100858600-100866400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:100858600-100880400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:100858600-100880400	Weak transcription	Brain Anterior Caudate	brain
18	chr9:100858800-100867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:100859000-100867000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:100859200-100880600	Weak transcription	Gastric	stomach
21	chr9:100860000-100869000	Strong transcription	Fetal Intestine Small	intestine
22	chr9:100860200-100880800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:100860600-100868000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:100861400-100868000	Enhancers	Primary hematopoietic stem cells	blood
25	chr9:100861400-100871800	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:100861400-100880600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:100862200-100872200	Enhancers	Primary B cells from cord blood	blood
28	chr9:100862200-100872400	Weak transcription	Esophagus	oesophagus
29	chr9:100862400-100866200	Weak transcription	HepG2	liver
30	chr9:100862400-100866600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:100862400-100866800	Weak transcription	Fetal Stomach	stomach
32	chr9:100862400-100867000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:100862400-100867000	Weak transcription	Spleen	Spleen
34	chr9:100862400-100867200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:100862400-100867200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:100862400-100867200	Weak transcription	Lung	lung
37	chr9:100862400-100869000	Weak transcription	K562	blood
38	chr9:100862400-100869600	Weak transcription	Adipose Nuclei	Adipose
39	chr9:100862400-100871800	Weak transcription	HMEC	breast
40	chr9:100862400-100880000	Weak transcription	Small Intestine	intestine
41	chr9:100862400-100880600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:100862600-100866200	Weak transcription	Liver	Liver
43	chr9:100862600-100869000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr9:100862800-100867000	Weak transcription	Colonic Mucosa	Colon
45	chr9:100863000-100866200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:100863000-100866400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr9:100863000-100866800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:100863600-100865000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr9:100863600-100865000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:100863600-100866200	Weak transcription	Fetal Intestine Large	intestine

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