Variant report

Variant	rs12238477
Chromosome Location	chr9:96423510-96423511
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96415816..96418876-chr9:96421256..96423559,3	MCF-7	breast:
2	chr9:96421764..96424036-chr9:96427270..96429397,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10992808	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992809	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992811	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992816	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992826	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992827	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992830	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992833	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992834	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992862	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12235863	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237139	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237261	1.00[EUR][1000 genomes]
rs16912647	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1806673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2398852	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3750353	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750356	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750360	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9644970	1.00[AMR][1000 genomes];1.00[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	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
2	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
3	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
4	nsv972421	chr9:96413056-96428661	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3341449	chr9:96421831-96426729	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96392200-96423600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:96399400-96423600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr9:96400400-96430600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr9:96401000-96430000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:96401000-96438600	Weak transcription	Psoas Muscle	Psoas
6	chr9:96402600-96430200	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:96402600-96433600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:96403400-96430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:96403400-96430800	Strong transcription	Liver	Liver
10	chr9:96405000-96423800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:96405200-96423600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr9:96405200-96429200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr9:96405200-96431400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:96405400-96423600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:96405400-96423600	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr9:96405400-96430000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr9:96405400-96430600	Strong transcription	Primary T cells from cord blood	blood
18	chr9:96405400-96431400	Strong transcription	Fetal Brain Female	brain
19	chr9:96405400-96433200	Strong transcription	Fetal Intestine Small	intestine
20	chr9:96405600-96429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr9:96405600-96430000	Strong transcription	Brain Germinal Matrix	brain
22	chr9:96405600-96430400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:96405800-96423600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:96405800-96423800	Strong transcription	Ovary	ovary
25	chr9:96406200-96438600	Weak transcription	Small Intestine	intestine
26	chr9:96406600-96423600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr9:96406800-96430600	Strong transcription	Brain Hippocampus Middle	brain
28	chr9:96407200-96430400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:96407400-96423800	Strong transcription	Fetal Muscle Leg	muscle
30	chr9:96410000-96430200	Strong transcription	Fetal Muscle Trunk	muscle
31	chr9:96410200-96428600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:96410400-96432600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr9:96410400-96433200	Strong transcription	Gastric	stomach
34	chr9:96410800-96424000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:96411800-96428600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:96412400-96430000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:96412600-96423800	Strong transcription	Lung	lung
38	chr9:96412600-96427600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:96412600-96430000	Weak transcription	K562	blood
40	chr9:96412600-96439400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr9:96412600-96442800	Weak transcription	NHDF-Ad	bronchial
42	chr9:96412600-96445000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr9:96412800-96423800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr9:96412800-96423800	Weak transcription	Fetal Heart	heart
45	chr9:96412800-96425400	Weak transcription	Fetal Kidney	kidney
46	chr9:96412800-96425600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:96412800-96425800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:96412800-96427600	Weak transcription	Fetal Brain Male	brain
49	chr9:96412800-96430600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:96412800-96442800	Weak transcription	HMEC	breast

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