Variant report

Variant	rs3818934
Chromosome Location	chr6:109668480-109668481
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109668456..109674736-chr6:109696300..109702886,9	K562	blood:
2	chr6:109629710..109632603-chr6:109666871..109669752,2	K562	blood:
3	chr6:109667528..109670285-chr6:109670801..109673728,2	K562	blood:
4	chr6:109666475..109669130-chr6:109690489..109693013,2	K562	blood:
5	chr6:109665756..109668556-chr6:109669464..109671369,2	MCF-7	breast:
6	chr6:109666918..109669416-chr6:109676939..109680789,3	MCF-7	breast:
7	chr6:109665458..109673633-chr6:109699710..109704931,12	MCF-7	breast:
8	chr6:109667580..109670112-chr6:109691835..109693593,2	MCF-7	breast:
9	chr6:109665666..109669140-chr6:109702115..109705884,4	MCF-7	breast:
10	chr6:109659815..109666445-chr6:109666719..109672363,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203799	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10080429	0.91[EUR][1000 genomes]
rs1040284	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10457190	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1048203	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10782161	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782162	0.82[EUR][1000 genomes]
rs10872032	0.95[EUR][1000 genomes]
rs10872034	0.82[EUR][1000 genomes]
rs11153171	0.88[EUR][1000 genomes]
rs11153174	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153175	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153176	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153177	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153180	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153181	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11967108	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12190920	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12190996	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12192847	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12193493	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12197114	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12206928	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209691	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12213313	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12524273	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12524639	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528822	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13203252	0.80[AFR][1000 genomes]
rs13212766	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322816	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1358997	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1358998	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546980	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1590306	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17070580	0.91[EUR][1000 genomes]
rs1923725	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236582	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34202013	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35056702	0.91[EUR][1000 genomes]
rs36035949	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36099706	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757234	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778475	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778477	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3799839	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3807005	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59056467	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59906308	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68042406	0.83[EUR][1000 genomes]
rs6920962	0.83[EUR][1000 genomes]
rs6929023	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7372	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs752262	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7773095	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9320287	0.91[EUR][1000 genomes]
rs9480933	0.95[EUR][1000 genomes]
rs9480948	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480951	0.91[EUR][1000 genomes]
rs9480953	0.91[EUR][1000 genomes]
rs9480955	0.91[EUR][1000 genomes]
rs9480957	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487068	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9487094	0.91[EUR][1000 genomes]
rs9487095	0.91[EUR][1000 genomes]
rs9487097	0.87[EUR][1000 genomes]
rs9487098	0.88[EUR][1000 genomes]
rs9487100	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9885646	0.91[EUR][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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3818934	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs3818934	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs3818934	SMPD2	cis	Whole Blood	GTEx
rs3818934	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3818934	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
3	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
4	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:109654400-109668800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:109657800-109671000	Weak transcription	Lung	lung
8	chr6:109658400-109669200	Weak transcription	Liver	Liver
9	chr6:109658600-109670600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:109658800-109670600	Weak transcription	Right Atrium	heart
11	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
12	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
13	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:109661200-109668600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:109661400-109671400	Weak transcription	Fetal Thymus	thymus
16	chr6:109662600-109682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:109662800-109669600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:109662800-109670600	Weak transcription	Aorta	Aorta
19	chr6:109662800-109670600	Weak transcription	Right Ventricle	heart
20	chr6:109662800-109671000	Weak transcription	Psoas Muscle	Psoas
21	chr6:109662800-109677000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:109663000-109670600	Weak transcription	Adipose Nuclei	Adipose
23	chr6:109664000-109669000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:109664000-109670800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:109664200-109669000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:109664200-109670800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:109664200-109672800	Weak transcription	HSMM	muscle
28	chr6:109664400-109668600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:109664400-109670400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:109664400-109670600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:109664400-109671000	Weak transcription	Left Ventricle	heart
32	chr6:109665200-109669000	Weak transcription	K562	blood
33	chr6:109665600-109668600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:109665600-109669200	Weak transcription	Gastric	stomach
35	chr6:109665600-109670600	Weak transcription	Pancreas	Pancrea
36	chr6:109665600-109677000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:109665600-109680400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:109665800-109669000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:109665800-109669600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr6:109665800-109670600	Weak transcription	Fetal Muscle Leg	muscle
41	chr6:109666000-109669000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:109666000-109670800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:109666000-109678000	Weak transcription	Fetal Kidney	kidney
44	chr6:109666400-109669000	Weak transcription	Placenta	Placenta
45	chr6:109666400-109675200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:109666800-109668800	Weak transcription	HepG2	liver
47	chr6:109667000-109669800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:109667800-109671400	Enhancers	Fetal Intestine Small	intestine
49	chr6:109668000-109669200	Enhancers	Brain Substantia Nigra	brain
50	chr6:109668000-109671200	Enhancers	Rectal Mucosa Donor 31	rectum

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