Variant report

Variant	rs203883
Chromosome Location	chr6:28078356-28078357
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27775941..27778895-chr6:28077283..28079265,2	K562	blood:
2	chr6:27801194..27803769-chr6:28077806..28080000,2	K562	blood:
3	chr6:28077736..28080081-chr6:28112119..28113939,2	K562	blood:
4	chr6:28057160..28060114-chr6:28076848..28078710,3	K562	blood:
5	chr6:28060510..28063110-chr6:28077574..28080015,2	K562	blood:
6	chr6:27858238..27861004-chr6:28077246..28078908,2	K562	blood:
7	chr6:28072263..28073986-chr6:28075857..28078538,2	MCF-7	breast:
8	chr6:28074765..28079544-chr6:28088308..28092763,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203813	Chromatin interaction
ENSG00000196812	Chromatin interaction
ENSG00000219891	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1071893	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150666	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150678	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12173797	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1225592	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1225595	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1225716	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233691	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1233708	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs149955	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs149958	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149959	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149962	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149965	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs156738	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs156739	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1631552	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770131	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183244	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs188105	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203876	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203877	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203884	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203892	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203893	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622319	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2791332	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs476167	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs536704	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295760	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	nsv349384	chr6:28075886-28080766	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs203883	AL022393.7	cis	Nerve Tibial	GTEx
rs203883	AL022393.7	cis	Heart Left Ventricle	GTEx
rs203883	ZSCAN31	cis	Thyroid	GTEx
rs203883	AL022393.7	cis	Muscle Skeletal	GTEx
rs203883	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs203883	OR2B8P	cis	Thyroid	GTEx
rs203883	OR1F12	cis	Thyroid	GTEx
rs203883	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs203883	AL022393.7	cis	Artery Tibial	GTEx
rs203883	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28073000-28083800	Weak transcription	Aorta	Aorta
2	chr6:28073200-28081600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:28073200-28081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr6:28073200-28082200	Weak transcription	HSMM	muscle
5	chr6:28073200-28082400	Weak transcription	Fetal Stomach	stomach
6	chr6:28073200-28083000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:28073200-28083400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:28073200-28091400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:28073200-28091800	Weak transcription	Right Ventricle	heart
10	chr6:28073400-28080200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:28073400-28081200	Weak transcription	Adipose Nuclei	Adipose
12	chr6:28073400-28081600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:28073400-28081600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:28073400-28081600	Weak transcription	HSMMtube	muscle
15	chr6:28073400-28081600	Weak transcription	NH-A	brain
16	chr6:28073400-28081800	Weak transcription	Primary B cells from cord blood	blood
17	chr6:28073400-28082000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:28073400-28082000	Weak transcription	Fetal Thymus	thymus
19	chr6:28073400-28082200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:28073400-28082200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:28073400-28082200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:28073400-28082200	Weak transcription	GM12878-XiMat	blood
23	chr6:28073400-28082400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:28073400-28082400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr6:28073400-28082400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:28073400-28082400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:28073400-28082600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:28073400-28082600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:28073400-28082600	Weak transcription	Placenta	Placenta
30	chr6:28073400-28082800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:28073400-28082800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:28073400-28083000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:28073400-28083000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:28073400-28083000	Weak transcription	Fetal Lung	lung
35	chr6:28073400-28083000	Weak transcription	Thymus	Thymus
36	chr6:28073400-28083000	Weak transcription	Spleen	Spleen
37	chr6:28073400-28083200	Weak transcription	Brain Angular Gyrus	brain
38	chr6:28073400-28083400	Weak transcription	A549	lung
39	chr6:28073400-28083600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:28073400-28083600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:28073400-28083600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:28073400-28083600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:28073400-28083600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:28073400-28083600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:28073400-28083600	Weak transcription	Fetal Kidney	kidney
46	chr6:28073400-28083800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:28073400-28083800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:28073400-28088000	Weak transcription	NHLF	lung
49	chr6:28073400-28091200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:28073400-28091400	Weak transcription	NHDF-Ad	bronchial

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