Variant report

Variant	rs1376027
Chromosome Location	chr3:150166817-150166818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150166057..150167740-chr3:150189958..150192196,2	K562	blood:
2	chr3:150125330..150128900-chr3:150162907..150168897,9	MCF-7	breast:
3	chr3:150159261..150162412-chr3:150164132..150166856,3	MCF-7	breast:
4	chr3:149955639..149959111-chr3:150165929..150170127,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244541	Chromatin interaction
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10513368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513370	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513372	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713072	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11714034	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11714123	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11925759	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11928577	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066114	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067910	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068946	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073230	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs13076419	0.92[CEU][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089766	0.87[EUR][1000 genomes]
rs13317818	0.89[ASN][1000 genomes]
rs17278131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28571974	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28587291	0.89[ASN][1000 genomes]
rs2868430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34106738	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34156311	0.93[ASN][1000 genomes]
rs34419133	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503712	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34647320	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34983941	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35019980	0.87[EUR][1000 genomes]
rs35234277	0.82[ASN][1000 genomes]
rs35598887	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3749400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811719	0.89[ASN][1000 genomes]
rs61734437	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66816665	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67073112	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67100311	0.87[EUR][1000 genomes]
rs6791546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799106	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73165716	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73167540	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7614772	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618493	0.89[ASN][1000 genomes]
rs7620193	0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7621019	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7623100	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827736	0.82[ASN][1000 genomes]
rs9844735	0.89[ASN][1000 genomes]
rs9875752	0.89[ASN][1000 genomes]
rs9879140	0.89[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	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1376027	TSC22D2	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150132400-150175000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:150132400-150175000	Weak transcription	Placenta	Placenta
3	chr3:150134600-150174800	Weak transcription	Dnd41	blood
4	chr3:150135000-150175600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:150137200-150176200	Weak transcription	HepG2	liver
6	chr3:150140000-150171800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:150140000-150176200	Weak transcription	Fetal Stomach	stomach
8	chr3:150141400-150175200	Weak transcription	GM12878-XiMat	blood
9	chr3:150144200-150179000	Weak transcription	Aorta	Aorta
10	chr3:150147000-150167200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:150149600-150176000	Weak transcription	Fetal Brain Female	brain
12	chr3:150151400-150171200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:150151400-150171600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:150151800-150167000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:150152200-150168800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:150152200-150171200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:150153000-150175600	Weak transcription	Right Ventricle	heart
18	chr3:150153600-150178200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:150153800-150176000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:150154000-150175800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:150154200-150176000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:150157800-150173000	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:150158600-150178200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:150159800-150171600	Weak transcription	Brain Substantia Nigra	brain
25	chr3:150159800-150175600	Weak transcription	Thymus	Thymus
26	chr3:150159800-150176200	Weak transcription	Spleen	Spleen
27	chr3:150160200-150175800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:150160400-150174800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:150160600-150176200	Weak transcription	Esophagus	oesophagus
30	chr3:150160600-150178000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:150160800-150168200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:150160800-150175200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:150160800-150175200	Weak transcription	Fetal Thymus	thymus
34	chr3:150160800-150175800	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:150160800-150176200	Weak transcription	Fetal Kidney	kidney
36	chr3:150160800-150176200	Weak transcription	Gastric	stomach
37	chr3:150161200-150174800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:150161400-150168600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:150161600-150168200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:150162000-150168600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr3:150162000-150168800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:150162200-150175000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:150162400-150174600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:150162400-150174800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:150162600-150168400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:150164400-150169600	Enhancers	Hela-S3	cervix
47	chr3:150164400-150169600	Enhancers	Osteobl	bone
48	chr3:150164600-150167000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:150164600-150169200	Enhancers	NHEK	skin
50	chr3:150164600-150169600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links