Variant report

Variant	rs6549181
Chromosome Location	chr3:69114370-69114371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:69114360-69115079	K562	blood:	n/a	n/a
2	POLR2A	chr3:69114349-69114931	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69114176..69116001-chr3:69116109..69118445,2	K562	blood:
2	chr3:69112430..69115275-chr3:69125875..69130297,4	MCF-7	breast:

Variant related genes	Relation type
UBA3	TF binding region
ENSG00000144744	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10489	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1051901	0.81[CHB][hapmap]
rs11128107	0.89[TSI][hapmap]
rs13063094	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090606	0.88[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13099820	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2009602	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271118	0.88[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.81[ASN][1000 genomes]
rs2271120	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs2271122	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279936	0.88[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2292198	0.82[AFR][1000 genomes]
rs2292199	0.82[CEU][hapmap];0.93[CHB][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35718539	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3755717	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755721	0.86[AFR][1000 genomes]
rs3772979	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772980	0.81[CHB][hapmap]
rs3796213	0.81[CHB][hapmap]
rs3821562	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3853157	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56156415	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58950441	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6549162	0.81[EUR][1000 genomes]
rs6549165	0.89[TSI][hapmap]
rs6549184	0.87[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6775065	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6775256	0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6777032	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782474	0.89[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6787569	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6807701	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs714300	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7611878	0.89[TSI][hapmap]
rs7615341	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625579	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9813514	0.94[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826616	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[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	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6549181	HOOK1	trans	lymphoblastoid	seeQTL
rs6549181	MEX3B	trans	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69101400-69127000	Weak transcription	Small Intestine	intestine
2	chr3:69101800-69128400	Weak transcription	Aorta	Aorta
3	chr3:69102000-69128200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:69102000-69128400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:69102200-69127200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:69102400-69116400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:69102800-69116600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:69103600-69116200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:69107400-69115600	Strong transcription	Liver	Liver
10	chr3:69107800-69115000	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:69108400-69128200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:69108600-69117000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:69108600-69121600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:69108600-69121600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:69108800-69115000	Strong transcription	Primary B cells from cord blood	blood
16	chr3:69109200-69114800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:69109200-69118000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:69109200-69121600	Weak transcription	Fetal Brain Male	brain
19	chr3:69110200-69127000	Weak transcription	Hela-S3	cervix
20	chr3:69110400-69120000	Weak transcription	HepG2	liver
21	chr3:69110400-69122000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:69110600-69127000	Weak transcription	Brain Angular Gyrus	brain
23	chr3:69110600-69127600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:69110600-69128200	Weak transcription	Right Ventricle	heart
25	chr3:69110600-69128400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:69110600-69128400	Weak transcription	Gastric	stomach
27	chr3:69110600-69128400	Weak transcription	Psoas Muscle	Psoas
28	chr3:69110800-69114600	Weak transcription	Fetal Stomach	stomach
29	chr3:69110800-69119800	Weak transcription	Ovary	ovary
30	chr3:69110800-69127000	Weak transcription	Pancreas	Pancrea
31	chr3:69110800-69127600	Weak transcription	Brain Substantia Nigra	brain
32	chr3:69110800-69127800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:69110800-69128600	Weak transcription	Esophagus	oesophagus
34	chr3:69110800-69128800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:69110800-69128800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:69111000-69116800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:69111000-69118400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:69111000-69119800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:69111000-69128600	Weak transcription	Lung	lung
40	chr3:69111000-69128800	Weak transcription	Spleen	Spleen
41	chr3:69111200-69121800	Weak transcription	Brain Anterior Caudate	brain
42	chr3:69111200-69128000	Weak transcription	K562	blood
43	chr3:69111200-69128200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:69111200-69128200	Weak transcription	Colonic Mucosa	Colon
45	chr3:69111400-69121600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:69111400-69121800	Weak transcription	Fetal Heart	heart
47	chr3:69111400-69122200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:69111400-69127000	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:69111400-69128400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr3:69111600-69117400	Weak transcription	Primary hematopoietic stem cells	blood

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