Variant report

Variant	rs4563951
Chromosome Location	chr9:96718590-96718591
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96709646..96715968-chr9:96715980..96721050,10	MCF-7	breast:
2	chr9:96718522..96721455-chr9:96725392..96727968,2	MCF-7	breast:
3	chr9:96713619..96716485-chr9:96717370..96719166,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPDC1-1	chr9:96718116-96719150	XLOC_007466

Variant related genes	Relation type
ENSG00000131668	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1057713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821273	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821274	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11788035	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11999521	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11999551	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12005806	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1320546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13283836	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13291289	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933680	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1933681	0.84[CHB][hapmap];0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1933682	0.84[AMR][1000 genomes]
rs2095778	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35001304	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4437716	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56285369	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7034685	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7872123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893589	chr9:96624645-96884544	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv824993	chr9:96699362-96725105	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893590	chr9:96701287-96729129	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3442102	chr9:96716156-96718704	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3412213	chr9:96716656-96718704	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96715000-96718800	Bivalent Enhancer	Spleen	Spleen
2	chr9:96716400-96718600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr9:96716400-96718600	Bivalent/Poised TSS	Fetal Stomach	stomach
4	chr9:96716400-96718800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr9:96717000-96718800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr9:96717000-96719200	Active TSS	Stomach Smooth Muscle	stomach
7	chr9:96717800-96718600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:96717800-96718600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:96717800-96718600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr9:96717800-96718600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:96717800-96718600	Bivalent Enhancer	Placenta	Placenta
12	chr9:96718000-96718600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr9:96718000-96718800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr9:96718000-96718800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
15	chr9:96718200-96718600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
16	chr9:96718200-96718600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:96718200-96718600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:96718200-96718600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:96718200-96718600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:96718200-96718600	Bivalent Enhancer	Brain Germinal Matrix	brain
21	chr9:96718200-96718600	Bivalent Enhancer	Brain Hippocampus Middle	brain
22	chr9:96718200-96718600	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr9:96718200-96719400	Active TSS	Gastric	stomach
24	chr9:96718400-96718600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
25	chr9:96718400-96718600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:96718400-96718600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr9:96718400-96718600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
28	chr9:96718400-96718600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
29	chr9:96718400-96718600	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr9:96718400-96718600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:96718400-96718600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:96718400-96718600	Bivalent Enhancer	Rectal Smooth Muscle	rectum
33	chr9:96718400-96718600	Flanking Active TSS	A549	lung
34	chr9:96718400-96718600	Flanking Bivalent TSS/Enh	Osteobl	bone
35	chr9:96718400-96718800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr9:96718400-96718800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
37	chr9:96718400-96718800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
38	chr9:96718400-96719000	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr9:96718400-96719000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr9:96718400-96719000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:96718400-96719200	Bivalent/Poised TSS	Stomach Mucosa	stomach
42	chr9:96718400-96719400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:96718400-96720800	Weak transcription	Right Atrium	heart
44	chr9:96718400-96721000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:96718400-96721200	Weak transcription	Pancreas	Pancrea
46	chr9:96718400-96722000	Weak transcription	Hela-S3	cervix

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