Variant report

Variant	rs6940
Chromosome Location	chr1:159024668-159024669
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:159023373-159027389	GM18505	blood:	n/a	n/a
2	POLR2A	chr1:159023796-159027402	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:159024320-159024857	U87	brain:	n/a	n/a
4	POLR2A	chr1:159023726-159024754	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:159023775-159024727	U87	brain:	n/a	n/a
6	POLR2A	chr1:159023708-159024745	U87	brain:	n/a	n/a
7	POLR2A	chr1:159019870-159029996	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:159023810-159024708	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:159020046-159029918	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:159023955-159024827	U87	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000265589	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11265134	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12098223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124059	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1616024	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1633266	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs1633267	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1772407	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2236584	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518555	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518562	0.82[CHB][hapmap]
rs2793844	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793845	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2852695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2852696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3018316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768514	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768519	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768523	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74122214	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74122232	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532207	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855865	0.86[JPT][hapmap];0.87[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	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6940	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
3	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
4	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
5	chr1:159000000-159026200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:159001000-159027400	Weak transcription	Right Ventricle	heart
7	chr1:159001400-159036200	Weak transcription	Small Intestine	intestine
8	chr1:159001600-159028400	Strong transcription	Fetal Thymus	thymus
9	chr1:159005600-159027200	Weak transcription	Brain Angular Gyrus	brain
10	chr1:159007200-159026800	Weak transcription	Pancreas	Pancrea
11	chr1:159009000-159026400	Strong transcription	Dnd41	blood
12	chr1:159009200-159030400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:159010600-159026400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:159013000-159025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:159016400-159024800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:159017000-159025600	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:159017000-159026800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:159018000-159026000	Strong transcription	Hela-S3	cervix
19	chr1:159018200-159026200	Strong transcription	Ovary	ovary
20	chr1:159019400-159025200	Strong transcription	Liver	Liver
21	chr1:159019400-159026200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:159019600-159024800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:159019600-159025000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:159019600-159025200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:159019600-159025400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr1:159019600-159025400	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr1:159019600-159026400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:159019800-159026000	Strong transcription	Adipose Nuclei	Adipose
29	chr1:159020000-159026200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:159020000-159026200	Strong transcription	Fetal Intestine Large	intestine
31	chr1:159020200-159025200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:159020200-159026000	Strong transcription	Fetal Lung	lung
33	chr1:159020200-159026800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:159020200-159027000	Strong transcription	Thymus	Thymus
35	chr1:159020200-159027200	Strong transcription	GM12878-XiMat	blood
36	chr1:159021000-159025400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:159021200-159028400	Weak transcription	Fetal Intestine Small	intestine
38	chr1:159021400-159024800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:159021400-159025600	Weak transcription	Fetal Stomach	stomach
40	chr1:159021400-159027000	Strong transcription	Rectal Smooth Muscle	rectum
41	chr1:159021800-159025600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:159021800-159028000	Weak transcription	Gastric	stomach
43	chr1:159022000-159025600	Weak transcription	Colonic Mucosa	Colon
44	chr1:159022200-159025800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:159022400-159025000	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:159022400-159028800	Weak transcription	Brain Substantia Nigra	brain
47	chr1:159022600-159026000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:159022600-159031600	Weak transcription	Fetal Brain Male	brain
49	chr1:159022800-159024800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:159022800-159025200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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