Variant report

Variant	rs7372
Chromosome Location	chr6:109688114-109688115
allele	C/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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109625270..109626980-chr6:109687907..109689980,2	K562	blood:
2	chr6:109415407..109417436-chr6:109687702..109689598,2	MCF-7	breast:
3	chr6:109684963..109689881-chr6:109693239..109697523,6	MCF-7	breast:
4	chr6:109687588..109690401-chr6:109719781..109721950,2	K562	blood:
5	chr6:109682199..109685973-chr6:109687053..109690833,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD164-1	chr6:109687717-109690220	NONHSAT114396

No data

Variant related genes	Relation type
ENSG00000080546	Chromatin interaction
ENSG00000201023	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10080429	0.91[EUR][1000 genomes]
rs1040284	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10457190	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1048203	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782161	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782162	0.83[EUR][1000 genomes]
rs10872032	0.95[EUR][1000 genomes]
rs10872034	0.83[EUR][1000 genomes]
rs11153171	0.87[EUR][1000 genomes]
rs11153174	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153175	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153176	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153177	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153180	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153181	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11967108	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12190920	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12190996	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12192847	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12193493	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197114	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12206928	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209691	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12213313	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12524273	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12524639	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528822	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13212766	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322816	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1358997	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1358998	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546980	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1590306	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17070580	0.92[EUR][1000 genomes]
rs1923725	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236582	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275650	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34202013	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35056702	0.92[EUR][1000 genomes]
rs36035949	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36099706	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757234	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778475	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778477	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799839	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807005	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3818934	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59056467	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59906308	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68042406	0.83[EUR][1000 genomes]
rs6911838	0.80[EUR][1000 genomes]
rs6920962	0.84[EUR][1000 genomes]
rs6929023	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752262	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773095	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9320287	0.92[EUR][1000 genomes]
rs9480933	0.95[EUR][1000 genomes]
rs9480948	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480951	0.92[EUR][1000 genomes]
rs9480953	0.92[EUR][1000 genomes]
rs9480955	0.92[EUR][1000 genomes]
rs9480957	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487068	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9487094	0.92[EUR][1000 genomes]
rs9487095	0.92[EUR][1000 genomes]
rs9487097	0.87[EUR][1000 genomes]
rs9487098	0.88[EUR][1000 genomes]
rs9487100	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9885646	0.92[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7372	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs7372	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs7372	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs7372	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs7372	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109675000-109691800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:109675000-109692600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:109675000-109693200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:109675000-109694400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr6:109675000-109694600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr6:109675000-109700800	Strong transcription	Placenta	Placenta
7	chr6:109675200-109688800	Strong transcription	Primary T cells from cord blood	blood
8	chr6:109675200-109693200	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:109675400-109691400	Strong transcription	Osteobl	bone
10	chr6:109676800-109693800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:109677000-109698200	Strong transcription	Fetal Intestine Large	intestine
12	chr6:109677600-109695000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:109677800-109700600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:109678200-109691400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:109678200-109694600	Strong transcription	Fetal Thymus	thymus
16	chr6:109678200-109695200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr6:109678400-109694400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:109678400-109694400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:109678600-109693200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:109678600-109693400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:109678800-109695400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr6:109678800-109699000	Strong transcription	Dnd41	blood
23	chr6:109679000-109688200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:109679000-109693200	Strong transcription	K562	blood
25	chr6:109679200-109700400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:109679400-109689000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:109679400-109700600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:109680400-109697200	Weak transcription	Fetal Brain Male	brain
29	chr6:109680600-109700600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:109680800-109688200	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:109680800-109694400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr6:109681000-109689400	Weak transcription	Brain Angular Gyrus	brain
33	chr6:109682400-109692600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:109682600-109700800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:109683200-109699800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:109683600-109692800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:109683800-109693400	Strong transcription	Primary B cells from cord blood	blood
38	chr6:109683800-109700600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:109684000-109688200	Weak transcription	Colonic Mucosa	Colon
40	chr6:109684000-109688200	Weak transcription	HepG2	liver
41	chr6:109684000-109688600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:109684000-109689200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:109684000-109689800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:109684000-109691000	Weak transcription	Fetal Brain Female	brain
45	chr6:109684000-109691200	Weak transcription	HSMMtube	muscle
46	chr6:109684000-109691400	Weak transcription	Brain Germinal Matrix	brain
47	chr6:109684000-109691600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr6:109684000-109692000	Weak transcription	Esophagus	oesophagus
49	chr6:109684000-109692800	Weak transcription	NHLF	lung
50	chr6:109684000-109693200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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