Variant report

Variant	rs6667049
Chromosome Location	chr1:10221847-10221848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1074461	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11121525	0.85[EUR][1000 genomes]
rs11806008	0.90[EUR][1000 genomes]
rs12074936	0.90[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs12092513	0.84[CHD][hapmap]
rs17034545	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs17034558	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs17034560	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2273298	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35316894	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3762290	0.83[JPT][hapmap]
rs4543799	0.94[ASW][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61782924	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61782933	0.81[ASN][1000 genomes]
rs61782936	0.81[ASN][1000 genomes]
rs61782937	0.81[ASN][1000 genomes]
rs61782938	0.81[ASN][1000 genomes]
rs6659436	0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs6671289	0.81[CEU][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes]
rs6692491	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9783053	0.89[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv522629	chr1:10125765-10239197	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6667049	UBE4B	cis	brain	BrainEAC
rs6667049	RERE	cis	parietal	SCAN
rs6667049	UBE4B	cis	intralobular white matter	BrainEAC
rs6667049	NOL9	cis	parietal	SCAN
rs6667049	LZIC	cis	lymphoblastoid	seeQTL
rs6667049	UBE4B	cis	cerebellum	SCAN
rs6667049	UBE4B	cis	temporal cortex	BrainEAC
rs6667049	UBE4B	cis	cerebellar cortex	BrainEAC
rs6667049	UBE4B	cis	parietal	SCAN
rs6667049	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs6667049	KIF1B	cis	parietal	SCAN
rs6667049	UBE4B	cis	hippocampus	BrainEAC
rs6667049	LZIC	cis	Lymphoblastoid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10164000-10227400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:10182200-10231200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:10182400-10229400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:10182800-10231400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:10184000-10235000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:10191200-10225000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:10191200-10239600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:10193200-10231200	Weak transcription	Small Intestine	intestine
9	chr1:10194200-10232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:10195600-10231200	Weak transcription	HUVEC	blood vessel
11	chr1:10197600-10225000	Weak transcription	NHEK	skin
12	chr1:10197800-10224400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:10197800-10224800	Weak transcription	Esophagus	oesophagus
14	chr1:10201600-10231200	Weak transcription	HMEC	breast
15	chr1:10203400-10228000	Weak transcription	GM12878-XiMat	blood
16	chr1:10204200-10224800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:10205600-10228000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:10207200-10224400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:10207400-10224800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:10211200-10222000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:10211200-10236400	Strong transcription	Fetal Stomach	stomach
22	chr1:10212000-10222600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:10212000-10224800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:10212000-10224800	Weak transcription	Fetal Kidney	kidney
25	chr1:10212000-10225000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:10213000-10224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:10213200-10231000	Weak transcription	A549	lung
28	chr1:10213400-10222600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:10213800-10236000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr1:10214600-10235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:10214600-10237000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:10215200-10229200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:10215400-10225400	Weak transcription	NHLF	lung
34	chr1:10215400-10234400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:10215600-10225000	Weak transcription	HSMM	muscle
36	chr1:10216000-10225400	Weak transcription	Right Ventricle	heart
37	chr1:10216200-10236400	Strong transcription	Placenta	Placenta
38	chr1:10217800-10226800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:10217800-10230200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:10218000-10222400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:10218000-10223800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:10218000-10226600	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:10218000-10226800	Strong transcription	Primary T cells from cord blood	blood
44	chr1:10218000-10226800	Strong transcription	Fetal Thymus	thymus
45	chr1:10218000-10226800	Strong transcription	Lung	lung
46	chr1:10218000-10234600	Strong transcription	Liver	Liver
47	chr1:10218200-10223600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:10218200-10226600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:10218200-10229600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:10218200-10235800	Strong transcription	Fetal Muscle Trunk	muscle

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