Variant report

Variant	rs12038135
Chromosome Location	chr1:62249367-62249368
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10889256	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11207831	0.85[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs11207837	0.85[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11207842	0.84[EUR][1000 genomes]
rs12045055	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12135784	1.00[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs12403946	0.85[EUR][1000 genomes]
rs12407806	0.82[EUR][1000 genomes]
rs3790576	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs3790577	0.94[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4915776	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4915778	0.82[GIH][hapmap];0.87[TSI][hapmap]
rs4915781	0.89[EUR][1000 genomes]
rs4915782	0.82[EUR][1000 genomes]
rs61770137	0.85[EUR][1000 genomes]
rs6661185	0.88[EUR][1000 genomes]
rs7516332	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs7519647	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs7530529	0.81[EUR][1000 genomes]
rs9645411	0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12038135	ST3GAL6	trans	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62210000-62253400	Weak transcription	Pancreas	Pancrea
2	chr1:62212200-62254400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:62212800-62255400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:62213600-62253000	Weak transcription	Fetal Kidney	kidney
5	chr1:62213600-62263200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:62217600-62254600	Weak transcription	Fetal Stomach	stomach
7	chr1:62220200-62290200	Weak transcription	Lung	lung
8	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:62221800-62263000	Weak transcription	Colonic Mucosa	Colon
10	chr1:62222000-62293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:62222200-62260800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:62222800-62258400	Weak transcription	Esophagus	oesophagus
13	chr1:62224000-62263000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:62224000-62267600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:62224000-62290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:62224400-62253400	Weak transcription	Ovary	ovary
17	chr1:62224600-62263000	Weak transcription	Left Ventricle	heart
18	chr1:62225000-62284400	Weak transcription	Psoas Muscle	Psoas
19	chr1:62227800-62294600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
21	chr1:62230600-62253600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:62231800-62273400	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:62232200-62262800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:62232800-62267200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:62233000-62263000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:62233200-62263800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:62233400-62254800	Weak transcription	Fetal Lung	lung
28	chr1:62233400-62264200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:62233400-62288800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:62235400-62253200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:62235400-62253400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:62235400-62263200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:62235400-62288800	Weak transcription	A549	lung
34	chr1:62235600-62253400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:62235600-62253400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:62237400-62251800	Weak transcription	Aorta	Aorta
37	chr1:62237600-62263000	Weak transcription	Fetal Brain Female	brain
38	chr1:62237800-62253400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:62239200-62253000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:62239400-62258800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:62240200-62264600	Weak transcription	Right Ventricle	heart
42	chr1:62240800-62264800	Weak transcription	Hela-S3	cervix
43	chr1:62242000-62261600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:62242200-62274400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:62242400-62253400	Weak transcription	HepG2	liver
46	chr1:62243000-62270600	Weak transcription	Spleen	Spleen
47	chr1:62243200-62253200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:62244000-62252600	Weak transcription	Fetal Intestine Large	intestine
49	chr1:62245800-62249800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:62245800-62251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links