Variant report

Variant	rs9390026
Chromosome Location	chr6:143201273-143201274
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	chr6:143201225..143204223-chr6:143212902..143216834,4	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1005294	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs107118	0.82[ASN][1000 genomes]
rs107119	0.82[ASN][1000 genomes]
rs13195550	0.98[GIH][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap]
rs13209704	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13211716	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198669	0.86[ASN][1000 genomes]
rs198670	0.86[ASN][1000 genomes]
rs198671	0.87[ASN][1000 genomes]
rs198673	0.86[ASN][1000 genomes]
rs198674	0.87[ASN][1000 genomes]
rs198676	0.87[ASN][1000 genomes]
rs198679	0.89[ASN][1000 genomes]
rs198680	0.89[ASN][1000 genomes]
rs2050311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28743065	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896599	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5022324	0.82[ASN][1000 genomes]
rs67253362	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6925325	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs728035	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8180684	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321878	0.85[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9376710	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9390025	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403408	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs9496470	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9496471	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][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	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9390026	FUCA2	cis	lymphoblastoid	seeQTL
rs9390026	C6orf115	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143188600-143206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:143189400-143201400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:143189400-143205400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr6:143189400-143205800	Weak transcription	Fetal Stomach	stomach
5	chr6:143189600-143204200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:143191200-143205600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:143193400-143203800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:143193600-143201400	Weak transcription	NHLF	lung
9	chr6:143193600-143204200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:143194000-143203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:143194200-143202200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:143194200-143204000	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:143194200-143204600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:143195200-143204200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:143195200-143206000	Weak transcription	Aorta	Aorta
16	chr6:143196000-143202800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:143196200-143204400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:143196200-143205200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:143196200-143205600	Weak transcription	HUVEC	blood vessel
20	chr6:143196400-143202000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:143196400-143202600	Weak transcription	NH-A	brain
22	chr6:143196400-143202800	Weak transcription	Placenta	Placenta
23	chr6:143196400-143202800	Weak transcription	Osteobl	bone
24	chr6:143196400-143203000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:143196400-143204800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:143196400-143205600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:143196400-143205600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr6:143196400-143205600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:143196400-143205600	Weak transcription	NHEK	skin
30	chr6:143196600-143202600	Weak transcription	Fetal Intestine Small	intestine
31	chr6:143196600-143204400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:143196600-143205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:143196600-143206000	Weak transcription	HepG2	liver
34	chr6:143196800-143205800	Weak transcription	Spleen	Spleen
35	chr6:143196800-143206000	Weak transcription	Stomach Mucosa	stomach
36	chr6:143197000-143201400	Weak transcription	Small Intestine	intestine
37	chr6:143197000-143205800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:143197000-143205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:143198600-143201800	Strong transcription	Primary T cells from cord blood	blood
40	chr6:143199000-143201800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:143199000-143202000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:143199000-143203800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:143199200-143202000	Enhancers	Brain Angular Gyrus	brain
44	chr6:143199600-143201400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:143199600-143202000	Enhancers	Left Ventricle	heart
46	chr6:143199600-143202000	Enhancers	Psoas Muscle	Psoas
47	chr6:143199600-143202200	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr6:143199600-143202200	Enhancers	Fetal Muscle Leg	muscle
49	chr6:143199600-143202200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:143199600-143202600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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