Variant report

Variant	rs4342141
Chromosome Location	chr3:160783922-160783923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160783848..160785805-chr3:160786120..160789700,3	MCF-7	breast:
2	chr3:160783790..160785578-chr3:161057040..161058658,2	MCF-7	breast:
3	chr3:160759280..160760955-chr3:160782590..160785077,2	MCF-7	breast:
4	chr3:160778095..160780488-chr3:160782527..160784697,2	K562	blood:
5	chr3:160783004..160785203-chr3:160947837..160949834,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1026572	0.89[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs1037888	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10513559	0.81[CEU][hapmap]
rs10936223	0.83[EUR][1000 genomes]
rs11716265	0.81[CEU][hapmap]
rs12631850	0.84[EUR][1000 genomes]
rs13064176	0.81[CEU][hapmap]
rs13066683	0.81[EUR][1000 genomes]
rs13086250	0.81[CEU][hapmap]
rs1599374	0.88[CEU][hapmap]
rs1599379	0.87[EUR][1000 genomes]
rs1599381	0.89[EUR][1000 genomes]
rs1599383	0.81[EUR][1000 genomes]
rs1599386	0.81[EUR][1000 genomes]
rs1599389	0.89[EUR][1000 genomes]
rs1599390	0.89[EUR][1000 genomes]
rs1610158	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs17826438	0.81[CEU][hapmap]
rs2306061	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs4557202	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs4618258	0.86[CEU][hapmap]
rs4679926	0.80[CEU][hapmap]
rs6441354	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6769642	0.82[EUR][1000 genomes]
rs6772578	0.82[EUR][1000 genomes]
rs6774635	0.81[EUR][1000 genomes]
rs6778254	0.81[EUR][1000 genomes]
rs6783085	0.89[EUR][1000 genomes]
rs6789244	0.89[EUR][1000 genomes]
rs6799130	0.88[EUR][1000 genomes]
rs6804650	0.81[CEU][hapmap]
rs6809177	0.81[CEU][hapmap]
rs7614375	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7617204	0.89[EUR][1000 genomes]
rs7619011	0.81[EUR][1000 genomes]
rs7622047	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7625363	0.87[EUR][1000 genomes]
rs7630768	0.89[EUR][1000 genomes]
rs7632423	0.81[CEU][hapmap]
rs7633857	0.89[EUR][1000 genomes]
rs7637086	0.89[EUR][1000 genomes]
rs7647285	0.88[EUR][1000 genomes]
rs7650703	0.81[EUR][1000 genomes]
rs7651087	0.89[EUR][1000 genomes]
rs778642	0.81[CEU][hapmap]
rs778653	0.81[CEU][hapmap]
rs796609	0.81[CEU][hapmap]
rs898680	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs898681	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs9290065	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9290069	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[EUR][1000 genomes]
rs9790132	0.81[CEU][hapmap]
rs980975	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs980976	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs9811594	0.81[CEU][hapmap]
rs9820825	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs9847866	0.82[CEU][hapmap]
rs9848239	0.81[EUR][1000 genomes]
rs9867582	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4342141	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160768000-160786400	Weak transcription	Left Ventricle	heart
2	chr3:160772000-160784200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:160773200-160786800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:160773600-160785600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:160773800-160787200	Weak transcription	Gastric	stomach
6	chr3:160776000-160787200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:160777200-160787800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:160778200-160786400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:160779200-160785200	Weak transcription	Aorta	Aorta
10	chr3:160780400-160788600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:160780600-160786400	Weak transcription	Primary T cells from cord blood	blood
12	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
13	chr3:160781200-160786600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:160781400-160785400	Weak transcription	Pancreas	Pancrea
15	chr3:160781400-160803400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:160781600-160788000	Weak transcription	Psoas Muscle	Psoas
17	chr3:160781600-160791000	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:160781800-160787200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:160781800-160787400	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:160781800-160798200	Weak transcription	Fetal Stomach	stomach
21	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
22	chr3:160782000-160799800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:160782200-160785200	Weak transcription	Adipose Nuclei	Adipose
24	chr3:160782600-160784000	Enhancers	Esophagus	oesophagus
25	chr3:160782600-160784000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:160782600-160785600	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:160782600-160786400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:160782600-160787200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:160782800-160795000	Weak transcription	Right Ventricle	heart
30	chr3:160783200-160784000	Strong transcription	Brain Germinal Matrix	brain
31	chr3:160783200-160784000	Strong transcription	Rectal Smooth Muscle	rectum
32	chr3:160783200-160787200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:160783400-160787200	Weak transcription	Fetal Thymus	thymus
34	chr3:160783400-160787400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:160783400-160787400	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:160783400-160788600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:160783800-160784600	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:160783800-160787200	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links