Variant report

Variant	rs621569
Chromosome Location	chr9:136814445-136814446
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136813249..136815512-chr9:136856138..136859094,3	MCF-7	breast:
2	chr9:136814134..136815760-chr9:136832244..136834207,2	MCF-7	breast:
3	chr9:136813341..136815906-chr9:136834550..136837034,2	MCF-7	breast:
4	chr9:136737420..136739354-chr9:136812499..136814864,2	MCF-7	breast:
5	chr9:136810475..136813039-chr9:136813457..136816106,3	K562	blood:
6	chr9:136809153..136811030-chr9:136812692..136814573,2	MCF-7	breast:
7	chr9:136813385..136817177-chr9:136818574..136821004,3	MCF-7	breast:
8	chr9:136813894..136816969-chr9:136817141..136821146,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1633757	0.88[EUR][1000 genomes]
rs1768685	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471882	0.90[JPT][hapmap]
rs4744527	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs481964	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs485458	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs503596	0.89[CEU][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs532646	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557327	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562000	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578151	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs619173	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622543	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636541	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648353	0.90[JPT][hapmap]
rs687644	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688091	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs739449	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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	25 gene(s)	inside rSNPs	diseases
9	nsv466626	chr9:136807770-136835343	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv615742	chr9:136807770-136835343	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv831749	chr9:136809200-136915764	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs621569	C9orf163	cis	cerebellum	SCAN
rs621569	FCN1	cis	cerebellum	SCAN
rs621569	PNMA1	trans	parietal	SCAN
rs621569	C9orf98	cis	cerebellum	SCAN
rs621569	AGPAT2	cis	cerebellum	SCAN
rs621569	UBAC1	cis	parietal	SCAN
rs621569	MED27	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136784000-136819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:136801000-136815400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:136801200-136815600	Weak transcription	Right Atrium	heart
4	chr9:136801200-136815800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:136801200-136820200	Weak transcription	Left Ventricle	heart
6	chr9:136801400-136821200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:136802000-136815800	Weak transcription	Colonic Mucosa	Colon
8	chr9:136802200-136815800	Strong transcription	Fetal Intestine Small	intestine
9	chr9:136802800-136816200	Weak transcription	Fetal Kidney	kidney
10	chr9:136803000-136815200	Weak transcription	HSMMtube	muscle
11	chr9:136803200-136821200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:136803600-136821000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr9:136804200-136815400	Weak transcription	Ovary	ovary
14	chr9:136804200-136815400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr9:136804200-136819800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:136804200-136820200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:136804200-136821000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr9:136804200-136821200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:136804400-136814800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:136804400-136815000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:136805800-136819400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:136808400-136815600	Weak transcription	Brain Angular Gyrus	brain
23	chr9:136809600-136821000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:136809800-136814600	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr9:136810000-136815400	Weak transcription	NHLF	lung
26	chr9:136810200-136815000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:136810400-136815600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:136810400-136821200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:136810600-136815400	Weak transcription	HSMM	muscle
30	chr9:136810600-136815600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:136810600-136821200	Weak transcription	Osteobl	bone
32	chr9:136810800-136817400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:136810800-136818800	Weak transcription	Esophagus	oesophagus
34	chr9:136811200-136815800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:136811400-136820200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:136811400-136821000	Weak transcription	HMEC	breast
37	chr9:136811600-136814800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:136811600-136819800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr9:136811800-136815400	Weak transcription	Duodenum Mucosa	Duodenum
40	chr9:136811800-136816400	Weak transcription	Right Ventricle	heart
41	chr9:136811800-136818200	Weak transcription	Fetal Intestine Large	intestine
42	chr9:136811800-136821600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:136812000-136814600	Weak transcription	Liver	Liver
44	chr9:136812200-136817800	Weak transcription	NHEK	skin
45	chr9:136812200-136821800	Weak transcription	Hela-S3	cervix
46	chr9:136812400-136816000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:136813000-136817000	Enhancers	Fetal Lung	lung
48	chr9:136813200-136814600	Genic enhancers	Pancreas	Pancrea
49	chr9:136813200-136817000	Strong transcription	HepG2	liver
50	chr9:136813400-136814800	Enhancers	Fetal Brain Female	brain

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