Variant report

Variant	rs1805740
Chromosome Location	chr12:9075014-9075015
allele	A/C
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	chr12:9074891-9075657	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PHC1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10743564	0.89[ASN][1000 genomes]
rs10771204	0.85[JPT][hapmap]
rs10771216	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11048060	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805729	0.90[CEU][hapmap]
rs1805738	0.90[CEU][hapmap];0.91[GIH][hapmap]
rs1805741	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1805762	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1805776	0.89[CEU][hapmap]
rs1805778	0.80[JPT][hapmap]
rs3026261	0.90[CEU][hapmap];0.86[GIH][hapmap]
rs3809218	0.90[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4882967	0.84[ASN][1000 genomes]
rs4882970	0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs4883197	0.85[JPT][hapmap]
rs4883198	1.00[CEU][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4883199	0.80[JPT][hapmap]
rs4883200	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7297194	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1805740	PHC1	cis	Esophagus Muscularis	GTEx
rs1805740	PHC1	cis	Artery Aorta	GTEx
rs1805740	TAS2R43	cis	parietal	SCAN
rs1805740	LEPREL2	cis	parietal	SCAN
rs1805740	PHC1	cis	Artery Tibial	GTEx
rs1805740	M6PR	cis	parietal	SCAN
rs1805740	CLEC12B	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9068200-9079000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:9068200-9084000	Weak transcription	Esophagus	oesophagus
3	chr12:9068200-9086400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:9068200-9088800	Weak transcription	Gastric	stomach
5	chr12:9068200-9091400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:9068200-9094200	Weak transcription	Colonic Mucosa	Colon
7	chr12:9068200-9094200	Weak transcription	Lung	lung
8	chr12:9068200-9094200	Weak transcription	Psoas Muscle	Psoas
9	chr12:9068200-9094200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:9068200-9094200	Weak transcription	Small Intestine	intestine
11	chr12:9068200-9100000	Weak transcription	Stomach Mucosa	stomach
12	chr12:9068400-9075400	Weak transcription	A549	lung
13	chr12:9068600-9081200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:9068800-9081200	Weak transcription	NHDF-Ad	bronchial
15	chr12:9068800-9081600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr12:9068800-9084400	Weak transcription	Osteobl	bone
17	chr12:9068800-9086400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:9069000-9079600	Weak transcription	Fetal Brain Male	brain
19	chr12:9069000-9086400	Weak transcription	HepG2	liver
20	chr12:9069000-9094200	Weak transcription	NHLF	lung
21	chr12:9069400-9094000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:9069400-9094200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:9069600-9084400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr12:9069600-9092000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:9069800-9082400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:9069800-9083600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:9069800-9083800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:9070200-9076000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:9070400-9075800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr12:9070400-9078000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:9070400-9078800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:9070400-9079000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:9070400-9079600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:9070400-9083400	Weak transcription	K562	blood
35	chr12:9070400-9092000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:9070400-9092000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:9070600-9075800	Strong transcription	Placenta	Placenta
38	chr12:9070600-9078200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:9070600-9078200	Strong transcription	Fetal Thymus	thymus
40	chr12:9070600-9092000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:9070600-9092600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:9070600-9092600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:9071000-9075600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:9071000-9075600	Strong transcription	Fetal Stomach	stomach
45	chr12:9071000-9076000	Strong transcription	Colon Smooth Muscle	Colon
46	chr12:9071000-9076200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:9071000-9076200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:9071000-9076200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:9071000-9076200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:9071000-9076400	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links