Variant report

Variant	rs2001316
Chromosome Location	chr9:96394346-96394347
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96393648..96395801-chr9:96402500..96404793,2	MCF-7	breast:
2	chr9:96389762..96391845-chr9:96392211..96394395,2	K562	blood:
3	chr9:96385198..96387004-chr9:96393310..96394874,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10115715	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117599	0.81[EUR][1000 genomes]
rs10121780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992817	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992818	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992820	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992822	0.82[YRI][hapmap]
rs10992823	0.92[YRI][hapmap]
rs10992843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992863	0.82[TSI][hapmap]
rs1132003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12335855	0.90[EUR][1000 genomes]
rs12341126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12348927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349481	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12350966	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs12351976	0.90[EUR][1000 genomes]
rs12352026	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13440078	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13440115	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35137913	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3750364	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41276198	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41276204	0.90[EUR][1000 genomes]
rs55682342	0.89[EUR][1000 genomes]
rs55846473	0.82[ASN][1000 genomes]
rs72747414	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72747430	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72747446	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72747448	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72747451	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72747468	0.90[EUR][1000 genomes]
rs72747474	0.88[EUR][1000 genomes]
rs72747481	0.82[EUR][1000 genomes]
rs72747487	0.90[EUR][1000 genomes]
rs7869847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs9695734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1055035	chr9:96372269-96402747	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1036609	chr9:96375217-96477641	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv519449	chr9:96382100-96395429	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv893587	chr9:96383605-96451784	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96374600-96399800	Weak transcription	K562	blood
2	chr9:96380200-96411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:96380800-96399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:96384000-96396400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:96384600-96412200	Weak transcription	Stomach Mucosa	stomach
6	chr9:96387000-96411800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:96387200-96399800	Weak transcription	Fetal Heart	heart
8	chr9:96387600-96399600	Weak transcription	Fetal Kidney	kidney
9	chr9:96390200-96398800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr9:96390200-96405400	Weak transcription	HepG2	liver
11	chr9:96390400-96395200	Weak transcription	NHLF	lung
12	chr9:96390400-96398600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:96390400-96399400	Weak transcription	Hela-S3	cervix
14	chr9:96390600-96395200	Weak transcription	Brain Substantia Nigra	brain
15	chr9:96390600-96397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:96390600-96398200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:96390600-96398400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:96390600-96399000	Weak transcription	Osteobl	bone
19	chr9:96390600-96399600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:96390800-96396800	Weak transcription	NHEK	skin
21	chr9:96390800-96398400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr9:96390800-96398600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:96391400-96398800	Strong transcription	Fetal Intestine Small	intestine
24	chr9:96391400-96400800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:96391600-96395800	Strong transcription	Fetal Thymus	thymus
26	chr9:96391600-96398400	Strong transcription	Thymus	Thymus
27	chr9:96391600-96398600	Strong transcription	Fetal Intestine Large	intestine
28	chr9:96391600-96398800	Strong transcription	Aorta	Aorta
29	chr9:96391600-96399600	Strong transcription	Primary T cells from cord blood	blood
30	chr9:96391600-96399800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:96391600-96400200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:96391600-96400200	Strong transcription	Gastric	stomach
33	chr9:96391600-96402000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:96391800-96398800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:96391800-96399000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:96391800-96399000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:96391800-96400000	Strong transcription	Colonic Mucosa	Colon
38	chr9:96391800-96400400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:96391800-96400400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:96391800-96402400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:96391800-96402400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:96391800-96402400	Strong transcription	Placenta	Placenta
43	chr9:96392000-96396800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:96392000-96396800	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr9:96392000-96397000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:96392000-96397200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:96392000-96397200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:96392000-96397400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:96392000-96398000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr9:96392000-96398200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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