Variant report

Variant	rs1363333
Chromosome Location	chr5:112364945-112364946
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	chr5:112363970..112366861-chr5:112379639..112381179,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10039618	0.80[JPT][hapmap]
rs1057474	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11749921	0.84[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12517398	0.81[ASN][1000 genomes]
rs12654474	0.83[AFR][1000 genomes]
rs13156493	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs13159449	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13171553	0.81[AFR][1000 genomes]
rs13176362	0.84[AFR][1000 genomes]
rs13177101	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs13186334	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13445	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1549181	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17312754	0.84[AFR][1000 genomes]
rs17372511	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2112454	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs2227948	0.83[ASN][1000 genomes]
rs2416300	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3185733	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33544	0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs33551	0.86[JPT][hapmap];0.84[TSI][hapmap]
rs33552	0.81[JPT][hapmap]
rs33554	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs33557	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs33568	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs33569	0.80[CHB][hapmap]
rs3857434	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4073358	0.83[ASN][1000 genomes]
rs4073359	0.81[ASN][1000 genomes]
rs4074190	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4075350	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4301226	0.81[GIH][hapmap];0.85[JPT][hapmap]
rs4428399	0.83[ASN][1000 genomes]
rs4599529	0.82[GIH][hapmap]
rs4705745	0.83[ASN][1000 genomes]
rs4705749	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4705750	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705752	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705755	0.83[ASN][1000 genomes]
rs4705756	0.83[ASN][1000 genomes]
rs4705758	0.85[JPT][hapmap]
rs4778	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6594665	0.85[JPT][hapmap]
rs6869100	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6877769	0.83[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6893389	0.81[JPT][hapmap]
rs6894219	0.85[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6894937	0.81[ASN][1000 genomes]
rs7670	0.87[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7701781	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7731890	0.82[GIH][hapmap]
rs7732198	0.84[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs9122	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9784647	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1363333	MCC	cis	Whole Blood	GTEx
rs1363333	MCC	cis	cerebellum	SCAN
rs1363333	DCP2	cis	Skin Sun Exposed Lower leg	GTEx
rs1363333	DCP2	cis	multi-tissue	Pritchard
rs1363333	TSLP	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
5	chr5:112334000-112365200	Strong transcription	Placenta	Placenta
6	chr5:112349800-112366600	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:112352400-112367800	Strong transcription	Liver	Liver
8	chr5:112354600-112365400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:112356200-112365000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:112356200-112365000	Strong transcription	Adipose Nuclei	Adipose
11	chr5:112356400-112365400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:112358600-112365400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:112358800-112365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:112358800-112366000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:112359600-112365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:112359600-112365800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:112359600-112367800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:112359800-112365400	Strong transcription	Left Ventricle	heart
19	chr5:112359800-112365600	Strong transcription	Fetal Muscle Leg	muscle
20	chr5:112359800-112365800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:112360000-112365400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:112360000-112379000	Weak transcription	Small Intestine	intestine
23	chr5:112360200-112365400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr5:112360200-112368600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:112360400-112367200	Weak transcription	GM12878-XiMat	blood
26	chr5:112360400-112367600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:112360400-112368000	Weak transcription	Primary B cells from cord blood	blood
28	chr5:112360400-112368400	Weak transcription	Stomach Mucosa	stomach
29	chr5:112361000-112368000	Strong transcription	Fetal Stomach	stomach
30	chr5:112361400-112365400	Weak transcription	Right Atrium	heart
31	chr5:112361400-112365800	Strong transcription	Ovary	ovary
32	chr5:112361400-112365800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr5:112361400-112366200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:112361400-112367400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:112361400-112368200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:112361600-112365600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr5:112361800-112365000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:112361800-112365600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:112361800-112366000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr5:112362400-112365000	Strong transcription	Right Ventricle	heart
41	chr5:112362400-112365400	Weak transcription	Fetal Heart	heart
42	chr5:112362400-112365600	Strong transcription	Primary T cells from cord blood	blood
43	chr5:112362400-112365600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:112362400-112365800	Strong transcription	Esophagus	oesophagus
45	chr5:112362600-112365000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:112362800-112385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:112363000-112365800	Strong transcription	Thymus	Thymus
48	chr5:112363000-112374000	Weak transcription	Pancreas	Pancrea
49	chr5:112363200-112365400	Weak transcription	Brain Angular Gyrus	brain
50	chr5:112363200-112366200	Weak transcription	Placenta Amnion	Placenta Amnion

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