Variant report

Variant	rs3740946
Chromosome Location	chr11:58972669-58972670
allele	G/T
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:

Variant related genes	Relation type
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1048696	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10501375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10501376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896949	0.82[EUR][1000 genomes]
rs10896950	0.82[EUR][1000 genomes]
rs10896957	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11229868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229872	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229873	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229882	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229889	0.88[CEU][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs11229901	0.87[EUR][1000 genomes]
rs11229902	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11229903	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11229904	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12223401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12284370	0.82[EUR][1000 genomes]
rs12575770	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12576150	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12576412	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12576558	0.83[EUR][1000 genomes]
rs12576879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577252	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17153538	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1938595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35654554	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3781796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59466005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60265864	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61086875	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7104296	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7104437	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7926933	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7942203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869155	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3740946	MPEG1	cis	lymphoblastoid	seeQTL
rs3740946	WDR74	cis	parietal	SCAN
rs3740946	CCDC86	cis	parietal	SCAN
rs3740946	MPEG1	Cis_1M	lymphoblastoid	RTeQTL
rs3740946	DTX4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58943600-58975400	Weak transcription	NHEK	skin
2	chr11:58949400-58973400	Weak transcription	Right Ventricle	heart
3	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:58956400-58977400	Weak transcription	Hela-S3	cervix
5	chr11:58959600-58974600	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr11:58960400-58974800	Weak transcription	Aorta	Aorta
7	chr11:58962800-58975000	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr11:58963400-58973800	Weak transcription	Primary T cells from cord blood	blood
9	chr11:58964200-58976000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:58964400-58977400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:58964800-58975600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:58965800-58978000	Weak transcription	Left Ventricle	heart
13	chr11:58966000-58973200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr11:58966200-58973400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:58966600-58973800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:58966600-58973800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:58966600-58975400	Strong transcription	Fetal Muscle Leg	muscle
18	chr11:58966800-58974600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:58967000-58973000	Strong transcription	Fetal Brain Male	brain
20	chr11:58967000-58975000	Strong transcription	Fetal Brain Female	brain
21	chr11:58967200-58973800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:58968000-58973600	Strong transcription	Brain Anterior Caudate	brain
23	chr11:58968000-58975600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:58968400-58974200	Strong transcription	Ovary	ovary
25	chr11:58968400-58975800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:58968600-58973000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:58968800-58973800	Strong transcription	Brain Cingulate Gyrus	brain
28	chr11:58968800-58974400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr11:58969000-58973600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:58969000-58973800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:58969000-58974200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr11:58969000-58974400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:58969000-58974600	Strong transcription	Fetal Intestine Large	intestine
34	chr11:58969200-58973800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:58969200-58974200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:58969200-58974200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:58969200-58974200	Strong transcription	Liver	Liver
38	chr11:58969200-58974400	Strong transcription	Placenta	Placenta
39	chr11:58969200-58974600	Strong transcription	Fetal Kidney	kidney
40	chr11:58969400-58974400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:58969400-58975000	Strong transcription	Fetal Lung	lung
42	chr11:58969400-58975400	Weak transcription	HepG2	liver
43	chr11:58969600-58973400	Strong transcription	Brain Hippocampus Middle	brain
44	chr11:58970200-58973600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:58970400-58974000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:58971000-58973400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:58971200-58973400	Strong transcription	Brain Substantia Nigra	brain
48	chr11:58971200-58973800	Strong transcription	Colonic Mucosa	Colon
49	chr11:58971200-58975200	Strong transcription	Fetal Stomach	stomach
50	chr11:58971400-58973800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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