Variant report

Variant	rs12997093
Chromosome Location	chr2:172564438-172564439
allele	C/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	STAT3	chr2:172563986-172564547	MCF10A-Er-Src	breast:	n/a	n/a
2	REST	chr2:172564364-172564600	MCF-7	breast:	n/a	n/a
3	FOXA1	chr2:172564253-172564543	T-47D	breast:	n/a	n/a
4	FOXA1	chr2:172564352-172564508	T-47D	breast:	n/a	n/a
5	FOXA2	chr2:172564313-172564549	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:172562033..172564981-chr2:172949316..172951224,2	K562	blood:
2	chr2:172543004..172545570-chr2:172563636..172565451,2	K562	blood:
3	chr2:172562639..172565244-chr2:172948743..172950770,2	MCF-7	breast:

Variant related genes	Relation type
DYNC1I2	TF binding region
ENSG00000144355	Chromatin interaction
ENSG00000077380	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1028127	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10930491	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11690807	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052995	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12998411	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1607254	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17581284	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17614941	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271758	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2292816	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34242651	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34531723	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35854151	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770458	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4510184	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59844139	0.81[AMR][1000 genomes]
rs62184165	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6723259	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9789538	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12997093	SLC25A12	cis	parietal	SCAN
rs12997093	MAP1D	cis	parietal	SCAN
rs12997093	AC068039.4	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545000-172580200	Weak transcription	Pancreas	Pancrea
2	chr2:172545000-172580400	Weak transcription	Spleen	Spleen
3	chr2:172545000-172580800	Weak transcription	Gastric	stomach
4	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:172545800-172573000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:172545800-172575400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
9	chr2:172546000-172567800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:172546000-172568600	Weak transcription	Hela-S3	cervix
11	chr2:172546400-172574600	Weak transcription	Right Atrium	heart
12	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
13	chr2:172547000-172578600	Weak transcription	Fetal Brain Male	brain
14	chr2:172548200-172571800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:172548400-172579600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:172550200-172567800	Weak transcription	Dnd41	blood
17	chr2:172551600-172584400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:172552200-172573400	Weak transcription	Fetal Brain Female	brain
19	chr2:172552200-172587600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:172554000-172580200	Weak transcription	Aorta	Aorta
21	chr2:172554400-172566200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:172554400-172588000	Weak transcription	Esophagus	oesophagus
23	chr2:172554600-172572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:172554600-172572200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:172554800-172580400	Weak transcription	K562	blood
26	chr2:172555000-172566400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:172555000-172571800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:172555000-172571800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:172555000-172580200	Weak transcription	Brain Anterior Caudate	brain
30	chr2:172555600-172566400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:172556800-172568600	Weak transcription	Fetal Kidney	kidney
32	chr2:172557000-172566200	Weak transcription	Left Ventricle	heart
33	chr2:172557000-172568600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:172557000-172571800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:172557400-172584400	Weak transcription	Ovary	ovary
36	chr2:172557600-172572200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:172558000-172565200	Weak transcription	Fetal Stomach	stomach
38	chr2:172558000-172574600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:172558800-172571800	Weak transcription	Liver	Liver
40	chr2:172558800-172583400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr2:172559000-172568000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:172559000-172585000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:172559600-172566200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:172559600-172567800	Weak transcription	NHLF	lung
45	chr2:172559600-172572000	Weak transcription	GM12878-XiMat	blood
46	chr2:172559600-172605200	Weak transcription	Colonic Mucosa	Colon
47	chr2:172559800-172566600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:172559800-172571600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:172559800-172571600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:172559800-172571800	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links