Variant report

Variant	rs3741194
Chromosome Location	chr11:66626234-66626235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66382730..66385205-chr11:66623849..66626752,2	MCF-7	breast:
2	chr11:66623727..66626320-chr12:53294666..53297117,2	MCF-7	breast:
3	chr11:66623687..66627715-chr11:66700423..66703089,3	K562	blood:
4	chr11:66623956..66626628-chr11:66742603..66744450,3	K562	blood:
5	chr11:66625545..66627133-chr11:66822302..66823974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239306	Chromatin interaction
ENSG00000173237	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000170421	Chromatin interaction
ENSG00000266423	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160758	1.00[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs10750790	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10791889	0.95[CEU][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs10791892	0.83[EUR][1000 genomes]
rs10896135	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10896139	0.90[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs11227610	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11600959	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11601241	1.00[LWK][hapmap]
rs2077432	0.95[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2167457	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2187041	0.90[CEU][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs2380760	0.84[EUR][1000 genomes]
rs3741364	0.88[CHD][hapmap];0.83[GIH][hapmap]
rs4008953	0.86[EUR][1000 genomes]
rs4576826	0.83[EUR][1000 genomes]
rs4930184	0.83[EUR][1000 genomes]
rs4930390	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs6591222	0.90[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7103627	1.00[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs7119426	0.90[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs7120256	0.90[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs714766	0.83[EUR][1000 genomes]
rs7570	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs7930203	0.95[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7948839	0.85[CEU][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs9971487	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
8	nsv897795	chr11:66608521-66637926	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	esv3436093	chr11:66622376-66626574	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3741194	B3GNT1	cis	parietal	SCAN
rs3741194	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs3741194	EHBP1L1	cis	cerebellum	SCAN
rs3741194	VEGFB	cis	cerebellum	SCAN
rs3741194	RARRES3	cis	parietal	SCAN
rs3741194	C11orf80	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66624200-66626400	Weak transcription	Liver	Liver
2	chr11:66624200-66627000	Weak transcription	Stomach Mucosa	stomach
3	chr11:66624200-66645000	Weak transcription	Fetal Kidney	kidney
4	chr11:66624400-66627600	Weak transcription	Brain Substantia Nigra	brain
5	chr11:66624400-66630800	Weak transcription	NHEK	skin
6	chr11:66624400-66636000	Weak transcription	Primary T cells from cord blood	blood
7	chr11:66624400-66637400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:66624400-66640200	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:66624600-66628200	Weak transcription	Pancreas	Pancrea
10	chr11:66624800-66637400	Weak transcription	Aorta	Aorta
11	chr11:66625000-66627600	Enhancers	Fetal Brain Male	brain
12	chr11:66625000-66631200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr11:66625000-66636200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr11:66625000-66648800	Weak transcription	Right Atrium	heart
15	chr11:66625200-66627000	Weak transcription	Small Intestine	intestine
16	chr11:66625200-66627800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:66625200-66628400	Weak transcription	NHDF-Ad	bronchial
18	chr11:66625200-66628800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:66625200-66631200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:66625400-66626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:66625400-66626600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:66625400-66626600	Weak transcription	Spleen	Spleen
23	chr11:66625400-66626800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:66625400-66627400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
25	chr11:66625400-66627600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:66625400-66628200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:66625400-66628200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:66625400-66628200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr11:66625400-66628200	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr11:66625400-66628400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:66625400-66628400	Genic enhancers	Adipose Nuclei	Adipose
32	chr11:66625400-66629400	Weak transcription	Brain Angular Gyrus	brain
33	chr11:66625400-66629600	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:66625400-66630800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr11:66625400-66631200	Weak transcription	Brain Anterior Caudate	brain
36	chr11:66625400-66631600	Weak transcription	HSMMtube	muscle
37	chr11:66625400-66632000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr11:66625400-66632200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr11:66625400-66632800	Weak transcription	HepG2	liver
40	chr11:66625400-66634600	Strong transcription	Fetal Stomach	stomach
41	chr11:66625400-66636000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:66625400-66636000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:66625400-66642200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:66625400-66642200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:66625400-66645400	Weak transcription	Fetal Lung	lung
46	chr11:66625400-66645800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:66625400-66648000	Weak transcription	Left Ventricle	heart
48	chr11:66625400-66650600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:66625600-66626600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr11:66625600-66626600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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