Variant report

Variant	rs12073999
Chromosome Location	chr1:151753318-151753319
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151747349..151749226-chr1:151752622..151754895,2	K562	blood:
2	chr1:151733431..151735514-chr1:151752760..151754528,2	K562	blood:
3	chr1:151751164..151754159-chr1:151759156..151761091,3	MCF-7	breast:
4	chr1:151725664..151728632-chr1:151752750..151754620,2	MCF-7	breast:
5	chr1:151747348..151750868-chr1:151751909..151754177,3	MCF-7	breast:
6	chr1:151740448..151742418-chr1:151752436..151753955,2	MCF-7	breast:
7	chr1:151747349..151750061-chr1:151752622..151754355,2	K562	blood:
8	chr1:151752426..151754254-chr1:151778758..151780979,2	K562	blood:
9	chr1:151752203..151754340-chr1:151755695..151758408,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000249602	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000269621	Chromatin interaction
ENSG00000143450	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10888435	0.90[EUR][1000 genomes]
rs11204887	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204888	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12066445	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12409493	0.89[EUR][1000 genomes]
rs12567867	0.88[EUR][1000 genomes]
rs1781419	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2293088	0.89[EUR][1000 genomes]
rs33911740	0.90[EUR][1000 genomes]
rs3748612	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3923394	0.96[EUR][1000 genomes]
rs4845572	0.91[EUR][1000 genomes]
rs6667279	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7534811	0.90[EUR][1000 genomes]
rs868868	0.91[EUR][1000 genomes]
rs9017	0.88[EUR][1000 genomes]
rs9826	0.89[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12073999	TDRKH	Cis_1M	lymphoblastoid	RTeQTL
rs12073999	SNX27	cis	Esophagus Mucosa	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151736800-151762600	Weak transcription	Gastric	stomach
2	chr1:151737000-151762400	Weak transcription	Fetal Intestine Small	intestine
3	chr1:151737000-151762400	Weak transcription	HSMMtube	muscle
4	chr1:151737000-151762600	Weak transcription	Small Intestine	intestine
5	chr1:151737200-151753800	Weak transcription	A549	lung
6	chr1:151740800-151759000	Weak transcription	Esophagus	oesophagus
7	chr1:151741000-151762600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:151741200-151756200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:151742400-151755200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:151742800-151762600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:151744000-151762200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:151744600-151762200	Weak transcription	Primary B cells from cord blood	blood
13	chr1:151745400-151755600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:151745600-151754400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:151745600-151755400	Strong transcription	Primary T cells from cord blood	blood
16	chr1:151745800-151754600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:151745800-151754600	Strong transcription	Brain Germinal Matrix	brain
18	chr1:151745800-151755000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:151745800-151755400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:151745800-151755600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:151745800-151755600	Strong transcription	Dnd41	blood
22	chr1:151746000-151754600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:151746000-151762400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:151746200-151754600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:151746200-151754600	Strong transcription	Brain Anterior Caudate	brain
26	chr1:151746200-151754800	Strong transcription	Brain Hippocampus Middle	brain
27	chr1:151746200-151755200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:151746200-151755600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:151746200-151755600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:151746400-151753400	Strong transcription	Brain Cingulate Gyrus	brain
31	chr1:151746400-151754400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:151746400-151754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:151746800-151762000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:151747000-151762400	Weak transcription	Psoas Muscle	Psoas
35	chr1:151747000-151762400	Weak transcription	Right Ventricle	heart
36	chr1:151747200-151759600	Weak transcription	HMEC	breast
37	chr1:151747200-151762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:151747600-151762400	Weak transcription	Pancreas	Pancrea
39	chr1:151748400-151761400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:151748400-151762200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:151748600-151762400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:151748800-151754400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:151748800-151761800	Weak transcription	HepG2	liver
44	chr1:151748800-151762400	Weak transcription	Colonic Mucosa	Colon
45	chr1:151749000-151758800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:151749200-151755200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:151749200-151755800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:151749200-151762600	Weak transcription	Spleen	Spleen
49	chr1:151749400-151756400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:151749400-151762400	Weak transcription	Rectal Mucosa Donor 29	rectum

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