Variant report

Variant	rs12509305
Chromosome Location	chr4:89935386-89935387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89935095..89936816-chr4:89938623..89940372,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10031518	0.82[ASN][1000 genomes]
rs10433949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10470936	0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11097216	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11722033	0.86[ASN][1000 genomes]
rs11725475	0.86[ASN][1000 genomes]
rs11725938	0.81[ASN][1000 genomes]
rs11726708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12505427	1.00[ASN][1000 genomes]
rs12505696	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12507131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12508371	0.91[ASN][1000 genomes]
rs12508524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13129885	1.00[ASN][1000 genomes]
rs13146548	1.00[ASN][1000 genomes]
rs1398942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs1533292	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1533293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3733448	0.88[JPT][hapmap]
rs4367140	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs4627822	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs59684168	0.84[ASN][1000 genomes]
rs60770708	0.82[ASN][1000 genomes]
rs61315828	0.84[ASN][1000 genomes]
rs67850063	0.95[ASN][1000 genomes]
rs6817766	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6838424	0.80[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7691363	0.86[ASN][1000 genomes]
rs9307058	0.85[ASN][1000 genomes]
rs9790655	0.88[ASN][1000 genomes]
rs9994655	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89903000-89957200	Weak transcription	HSMM	muscle
2	chr4:89903400-89936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:89912200-89935800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:89912200-89943800	Weak transcription	Psoas Muscle	Psoas
5	chr4:89913400-89944000	Weak transcription	Gastric	stomach
6	chr4:89920400-89937000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:89921000-89950600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:89922400-89936000	Weak transcription	Adipose Nuclei	Adipose
9	chr4:89922600-89936800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:89922600-89949800	Weak transcription	HMEC	breast
11	chr4:89922800-89935800	Weak transcription	HUVEC	blood vessel
12	chr4:89922800-89945600	Weak transcription	A549	lung
13	chr4:89923400-89939400	Weak transcription	Primary T cells from cord blood	blood
14	chr4:89923600-89945600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:89923800-89936000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:89923800-89936000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:89923800-89937000	Weak transcription	Fetal Heart	heart
18	chr4:89923800-89943800	Weak transcription	Right Atrium	heart
19	chr4:89923800-89944400	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:89925400-89937000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:89925600-89939400	Weak transcription	Aorta	Aorta
22	chr4:89926000-89936000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:89926200-89936400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:89926400-89949600	Weak transcription	Left Ventricle	heart
25	chr4:89926600-89941000	Weak transcription	Esophagus	oesophagus
26	chr4:89926800-89951400	Weak transcription	Right Ventricle	heart
27	chr4:89928200-89936000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:89928400-89936400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:89928400-89940000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:89928600-89937800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:89928600-89941600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:89928800-89936000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:89928800-89939200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:89929000-89935800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:89929200-89939400	Weak transcription	HSMMtube	muscle
36	chr4:89930000-89942600	Weak transcription	Brain Anterior Caudate	brain
37	chr4:89931200-89944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:89931400-89936000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:89931600-89943600	Weak transcription	Small Intestine	intestine
40	chr4:89931600-89945400	Weak transcription	Liver	Liver
41	chr4:89931800-89936400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr4:89931800-89939400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:89932000-89937000	Weak transcription	K562	blood
44	chr4:89932200-89943800	Weak transcription	Pancreas	Pancrea
45	chr4:89932400-89935800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:89932400-89937200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:89932800-89939400	Weak transcription	NH-A	brain
48	chr4:89933400-89936000	Strong transcription	Fetal Muscle Leg	muscle
49	chr4:89933400-89936800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:89933600-89935800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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