Variant report

Variant	rs17723470
Chromosome Location	chr11:45227567-45227568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45225656..45227629-chr11:45228825..45231066,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10444286	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs10769123	0.82[ASW][hapmap];1.00[CHB][hapmap]
rs11038341	1.00[CHB][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs11038350	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11038357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12284404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3758723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940871	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Thyroid hormone levels	23408906	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17723470	PRDM11	cis	Thyroid	GTEx
rs17723470	DDB2	cis	parietal	SCAN
rs17723470	SYT13	cis	Thyroid	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45202800-45234000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:45203000-45237000	Weak transcription	Small Intestine	intestine
3	chr11:45203400-45230400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:45203400-45231000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:45203600-45231000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:45205200-45230400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:45205800-45238800	Weak transcription	HSMMtube	muscle
8	chr11:45205800-45251800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr11:45206000-45247800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:45206600-45251600	Weak transcription	HepG2	liver
11	chr11:45207000-45232400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr11:45207200-45230200	Weak transcription	Colonic Mucosa	Colon
13	chr11:45207600-45229400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:45209000-45235200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:45210000-45234200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:45210200-45227800	Weak transcription	Right Ventricle	heart
17	chr11:45210200-45230200	Weak transcription	Brain Angular Gyrus	brain
18	chr11:45210200-45247600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr11:45210200-45251600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:45210400-45229600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:45210400-45229600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:45210400-45230400	Weak transcription	Placenta	Placenta
23	chr11:45210400-45230400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:45210400-45230600	Weak transcription	Fetal Brain Male	brain
25	chr11:45210400-45230800	Weak transcription	Brain Substantia Nigra	brain
26	chr11:45210400-45230800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:45210400-45231200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr11:45210400-45232000	Weak transcription	Hela-S3	cervix
29	chr11:45210600-45229600	Weak transcription	Gastric	stomach
30	chr11:45211800-45229600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:45211800-45230200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr11:45211800-45231000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:45212800-45229800	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:45214400-45234800	Weak transcription	A549	lung
35	chr11:45214600-45231000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:45215600-45230200	Weak transcription	Psoas Muscle	Psoas
37	chr11:45215800-45230000	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:45215800-45231000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:45218600-45230000	Weak transcription	Fetal Kidney	kidney
40	chr11:45221200-45230600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:45221200-45231400	Weak transcription	Thymus	Thymus
42	chr11:45221800-45230400	Weak transcription	Ovary	ovary
43	chr11:45222600-45230200	Weak transcription	Fetal Lung	lung
44	chr11:45223400-45229600	Strong transcription	Fetal Intestine Small	intestine
45	chr11:45223400-45230800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:45223600-45229600	Strong transcription	Fetal Intestine Large	intestine
47	chr11:45224600-45231000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:45224800-45229600	Weak transcription	Aorta	Aorta
49	chr11:45224800-45247800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:45225200-45228800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links