Variant report

Variant	rs1048444
Chromosome Location	chr11:58973731-58973732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58939016..58941772-chr11:58971563..58975931,4	MCF-7	breast:
2	chr11:58937247..58940054-chr11:58973077..58975578,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10792228	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10896953	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896956	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10896958	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11229896	0.83[EUR][1000 genomes]
rs11229898	0.81[EUR][1000 genomes]
rs11229899	0.81[EUR][1000 genomes]
rs12280107	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17153461	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1938593	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1938594	0.86[CHB][hapmap]
rs1945592	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1945593	0.83[EUR][1000 genomes]
rs2000875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2211912	1.00[ASW][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs3847	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938915	0.84[EUR][1000 genomes]
rs4939260	0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4939263	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4939267	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4939269	0.80[MEX][hapmap]
rs5023474	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5023475	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61689139	0.83[EUR][1000 genomes]
rs656163	0.89[YRI][hapmap]
rs6591510	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6591515	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6591517	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7109866	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7111287	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7113607	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7121247	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7129035	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7129362	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7931234	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7938115	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1048444	UBE2L6	cis	parietal	SCAN
rs1048444	CYBASC3	cis	parietal	SCAN
rs1048444	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs1048444	CYBASC3	cis	cerebellum	SCAN
rs1048444	MPEG1	Cis_1M	lymphoblastoid	RTeQTL
rs1048444	SNORD28	cis	cerebellum	SCAN
rs1048444	TMX2	cis	cerebellum	SCAN
rs1048444	MPEG1	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58943600-58975400	Weak transcription	NHEK	skin
2	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:58956400-58977400	Weak transcription	Hela-S3	cervix
4	chr11:58959600-58974600	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr11:58960400-58974800	Weak transcription	Aorta	Aorta
6	chr11:58962800-58975000	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr11:58963400-58973800	Weak transcription	Primary T cells from cord blood	blood
8	chr11:58964200-58976000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:58964400-58977400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:58964800-58975600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:58965800-58978000	Weak transcription	Left Ventricle	heart
12	chr11:58966600-58973800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:58966600-58973800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr11:58966600-58975400	Strong transcription	Fetal Muscle Leg	muscle
15	chr11:58966800-58974600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:58967000-58975000	Strong transcription	Fetal Brain Female	brain
17	chr11:58967200-58973800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:58968000-58975600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr11:58968400-58974200	Strong transcription	Ovary	ovary
20	chr11:58968400-58975800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:58968800-58973800	Strong transcription	Brain Cingulate Gyrus	brain
22	chr11:58968800-58974400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr11:58969000-58973800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:58969000-58974200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr11:58969000-58974400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:58969000-58974600	Strong transcription	Fetal Intestine Large	intestine
27	chr11:58969200-58973800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:58969200-58974200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:58969200-58974200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:58969200-58974200	Strong transcription	Liver	Liver
31	chr11:58969200-58974400	Strong transcription	Placenta	Placenta
32	chr11:58969200-58974600	Strong transcription	Fetal Kidney	kidney
33	chr11:58969400-58974400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:58969400-58975000	Strong transcription	Fetal Lung	lung
35	chr11:58969400-58975400	Weak transcription	HepG2	liver
36	chr11:58970400-58974000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:58971200-58973800	Strong transcription	Colonic Mucosa	Colon
38	chr11:58971200-58975200	Strong transcription	Fetal Stomach	stomach
39	chr11:58971400-58973800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:58971400-58974400	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr11:58971400-58974600	Genic enhancers	Primary B cells from cord blood	blood
42	chr11:58971400-58974800	Strong transcription	Brain Germinal Matrix	brain
43	chr11:58971800-58973800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:58972000-58974600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:58972000-58974600	Strong transcription	Gastric	stomach
46	chr11:58972000-58975400	Strong transcription	Fetal Intestine Small	intestine
47	chr11:58972000-58977600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
48	chr11:58972200-58973800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr11:58972200-58973800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr11:58972400-58974600	Genic enhancers	Adipose Nuclei	Adipose

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