Variant report

Variant	rs1168311
Chromosome Location	chr12:66725912-66725913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:66723412..66726741-chr12:66727425..66730176,3	K562	blood:
2	chr12:66695061..66697885-chr12:66724006..66726002,2	K562	blood:
3	chr12:66712745..66714782-chr12:66724427..66727122,2	MCF-7	breast:
4	chr12:66720021..66726228-chr12:66728171..66733015,6	K562	blood:

Variant related genes	Relation type
ENSG00000127311	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1027399	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1027400	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1027401	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1039056	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1060724	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10784525	0.88[EUR][1000 genomes]
rs1168290	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168291	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168292	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168293	0.97[EUR][1000 genomes]
rs1168294	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168295	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168296	0.98[EUR][1000 genomes]
rs1168297	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168298	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168299	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168300	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168301	0.98[EUR][1000 genomes]
rs1168302	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168303	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168304	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168305	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168306	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168307	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168309	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168310	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1168314	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168315	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168316	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168317	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1168318	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168319	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168320	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168321	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168322	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1168325	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168330	0.92[EUR][1000 genomes]
rs1168332	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168333	0.94[EUR][1000 genomes]
rs1168334	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168338	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168339	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168340	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168341	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168342	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168343	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168344	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168345	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168346	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168347	0.93[EUR][1000 genomes]
rs1168348	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168351	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168352	0.96[EUR][1000 genomes]
rs1168353	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168356	0.96[EUR][1000 genomes]
rs1168357	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168358	0.96[EUR][1000 genomes]
rs1177555	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1179889	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1183272	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1183274	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1184551	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1184552	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1185244	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495497	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1625394	0.84[CEU][hapmap]
rs1795527	0.87[EUR][1000 genomes]
rs1795529	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2172881	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2951656	0.96[EUR][1000 genomes]
rs4762091	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61925898	0.83[EUR][1000 genomes]
rs6581677	0.92[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6581678	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs903587	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs903589	0.96[EUR][1000 genomes]
rs903590	0.96[EUR][1000 genomes]
rs961049	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1168311	HMGA2	cis	parietal	SCAN
rs1168311	HELB	cis	parietal	SCAN
rs1168311	HELB	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66696800-66734200	Weak transcription	HSMMtube	muscle
2	chr12:66697200-66733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr12:66697200-66734800	Weak transcription	Esophagus	oesophagus
4	chr12:66697200-66735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:66697400-66732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:66697400-66732400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:66697400-66735000	Weak transcription	Right Ventricle	heart
9	chr12:66698200-66735000	Weak transcription	Fetal Brain Female	brain
10	chr12:66698400-66732400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:66698400-66734800	Weak transcription	HepG2	liver
12	chr12:66699000-66735000	Weak transcription	K562	blood
13	chr12:66702600-66734800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:66704200-66733600	Weak transcription	A549	lung
15	chr12:66704200-66735000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:66704400-66732200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:66704400-66733600	Weak transcription	Brain Anterior Caudate	brain
18	chr12:66704400-66741800	Weak transcription	Hela-S3	cervix
19	chr12:66705000-66729000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:66705200-66730200	Weak transcription	Left Ventricle	heart
21	chr12:66705200-66731800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:66705800-66732400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:66705800-66732600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:66705800-66734800	Weak transcription	Fetal Stomach	stomach
25	chr12:66706200-66732600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:66708200-66732400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:66709400-66727800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:66710200-66733400	Weak transcription	Fetal Lung	lung
29	chr12:66710200-66792800	Weak transcription	Fetal Kidney	kidney
30	chr12:66713600-66727600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:66714600-66733600	Strong transcription	Primary T cells from cord blood	blood
32	chr12:66714800-66728200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:66715400-66727400	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:66715600-66733600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:66715600-66734800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:66715600-66736600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:66716000-66733400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:66716400-66727600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:66716600-66734800	Weak transcription	NH-A	brain
40	chr12:66717400-66732400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr12:66717400-66733400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:66719600-66731800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:66721400-66733600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:66721400-66734800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr12:66721800-66733600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr12:66722600-66735000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:66723000-66727200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:66723000-66727400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:66723200-66734800	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:66723400-66726000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood

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