Variant report

Variant	rs11970493
Chromosome Location	chr6:88261150-88261151
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88241091..88243670-chr6:88260945..88262832,2	K562	blood:
2	chr6:88256344..88258160-chr6:88260668..88262336,2	K562	blood:
3	chr6:88257019..88262069-chr6:88262854..88269707,6	K562	blood:
4	chr20:52532038..52534829-chr6:88258936..88261704,2	MCF-7	breast:
5	chr6:88259058..88262189-chr6:88264509..88268423,3	K562	blood:

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

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

rs_ID	r²[population]
rs12529993	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12530371	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34513746	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818057	0.81[AMR][1000 genomes]
rs4132446	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4354121	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707378	0.82[EUR][1000 genomes]
rs58305152	0.81[ASN][1000 genomes]
rs6454634	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6914244	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7759462	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444511	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9444513	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444514	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9444516	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444521	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9450719	0.83[AMR][1000 genomes]
rs9450728	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450729	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450734	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450735	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450740	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450741	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450743	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9450749	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450750	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450751	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450756	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9450760	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450763	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[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	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11970493	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr6:88228600-88262800	Weak transcription	Small Intestine	intestine
5	chr6:88228600-88271400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:88228600-88285200	Weak transcription	Spleen	Spleen
7	chr6:88228800-88269600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:88229400-88261600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:88229400-88271200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:88229600-88289000	Weak transcription	Lung	lung
11	chr6:88230000-88267000	Weak transcription	Brain Substantia Nigra	brain
12	chr6:88230400-88271200	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:88230800-88261600	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:88231200-88262800	Weak transcription	Brain Angular Gyrus	brain
15	chr6:88231200-88264200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:88240600-88268200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:88249000-88265600	Strong transcription	HepG2	liver
18	chr6:88249400-88263600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:88250000-88275200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:88250400-88262600	Weak transcription	HMEC	breast
21	chr6:88250600-88270800	Weak transcription	Fetal Heart	heart
22	chr6:88250600-88276800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:88250600-88281600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr6:88250800-88270400	Weak transcription	Pancreas	Pancrea
25	chr6:88251000-88281800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:88251000-88291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:88251200-88262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:88251200-88263400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:88251200-88270800	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:88251200-88271200	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:88251200-88275200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr6:88251200-88280000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:88251200-88280600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:88251200-88284800	Weak transcription	Stomach Mucosa	stomach
35	chr6:88251800-88261600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:88251800-88262600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:88251800-88263000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:88252200-88263000	Weak transcription	A549	lung
39	chr6:88253600-88274800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:88254200-88263000	Weak transcription	Hela-S3	cervix
41	chr6:88254200-88283600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr6:88254400-88262600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr6:88254600-88265000	Weak transcription	NHDF-Ad	bronchial
44	chr6:88254800-88261400	Weak transcription	Colonic Mucosa	Colon
45	chr6:88254800-88272000	Weak transcription	Fetal Brain Female	brain
46	chr6:88255000-88261400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:88255000-88261600	Weak transcription	Fetal Kidney	kidney
48	chr6:88255000-88262800	Weak transcription	Brain Anterior Caudate	brain
49	chr6:88255000-88263000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:88255000-88263200	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links