Variant report

Variant	rs9450741
Chromosome Location	chr6:88274353-88274354
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	chr6:88268495..88270215-chr6:88273834..88275381,2	MCF-7	breast:
2	chr6:88273263..88275318-chr6:88275795..88277791,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ORC3-2	chr6:88273570-88275290	NONHSAT113910

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11970493	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12529993	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12530371	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34513746	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818057	0.82[AMR][1000 genomes]
rs4132446	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4354121	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707378	0.84[EUR][1000 genomes]
rs58305152	0.85[ASN][1000 genomes]
rs6454634	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914244	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7759462	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444511	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444513	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444514	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444516	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444521	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9450719	0.84[AMR][1000 genomes]
rs9450728	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450729	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450734	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450735	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450740	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450743	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450749	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450750	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450751	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450756	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450760	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450763	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[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	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9450741	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88217800-88295800	Weak transcription	Fetal Brain Male	brain
2	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
3	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
5	chr6:88229600-88289000	Weak transcription	Lung	lung
6	chr6:88250000-88275200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:88250600-88276800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:88250600-88281600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr6:88251000-88281800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:88251000-88291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:88251200-88275200	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr6:88251200-88280000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:88251200-88280600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:88251200-88284800	Weak transcription	Stomach Mucosa	stomach
15	chr6:88253600-88274800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:88254200-88283600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:88256000-88284000	Weak transcription	Psoas Muscle	Psoas
18	chr6:88256200-88297600	Weak transcription	Right Ventricle	heart
19	chr6:88256400-88295800	Weak transcription	Gastric	stomach
20	chr6:88257600-88274800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:88258200-88274400	Strong transcription	Liver	Liver
22	chr6:88259600-88279800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:88260200-88277800	Weak transcription	NHEK	skin
24	chr6:88261000-88274800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:88261000-88276800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr6:88261200-88274400	Strong transcription	Dnd41	blood
27	chr6:88261200-88276800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:88261400-88275600	Strong transcription	Fetal Thymus	thymus
29	chr6:88261400-88276600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr6:88262000-88275400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:88262400-88279400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:88263200-88282200	Weak transcription	Small Intestine	intestine
33	chr6:88263400-88291400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:88264600-88282800	Weak transcription	Aorta	Aorta
35	chr6:88264600-88291000	Weak transcription	Brain Angular Gyrus	brain
36	chr6:88266800-88276400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:88267400-88274400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr6:88267400-88276800	Strong transcription	HepG2	liver
39	chr6:88268000-88274400	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:88268000-88279200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:88268200-88275600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr6:88269200-88276400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:88269400-88275400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:88269400-88278400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:88269600-88291400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:88270200-88274400	Strong transcription	Adipose Nuclei	Adipose
47	chr6:88270200-88274600	Strong transcription	Fetal Intestine Large	intestine
48	chr6:88270400-88278600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr6:88270800-88274400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:88271000-88274400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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