Variant report

Variant	rs2077408
Chromosome Location	chr11:93497279-93497280
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	chr11:93474520..93476254-chr11:93496960..93498891,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182919	Chromatin interaction
ENSG00000166012	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11020510	0.81[ASN][1000 genomes]
rs1150326	0.87[EUR][1000 genomes]
rs11822585	0.83[ASN][1000 genomes]
rs1807990	0.86[ASN][1000 genomes]
rs34057693	0.88[EUR][1000 genomes]
rs3763808	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55734929	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56364420	0.81[ASN][1000 genomes]
rs59031514	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598495	0.96[EUR][1000 genomes]
rs606087	0.83[EUR][1000 genomes]
rs606357	0.82[ASN][1000 genomes]
rs61498836	0.87[EUR][1000 genomes]
rs615428	0.81[EUR][1000 genomes]
rs61743303	0.83[ASN][1000 genomes]
rs61904953	0.88[EUR][1000 genomes]
rs61904957	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs628665	0.83[EUR][1000 genomes]
rs654896	0.87[EUR][1000 genomes]
rs664257	0.96[EUR][1000 genomes]
rs66460850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66483735	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66487029	0.88[EUR][1000 genomes]
rs66760087	0.88[EUR][1000 genomes]
rs66797025	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs669565	0.87[EUR][1000 genomes]
rs670391	0.87[EUR][1000 genomes]
rs67112133	0.83[ASN][1000 genomes]
rs67182840	0.84[ASN][1000 genomes]
rs67310816	0.83[ASN][1000 genomes]
rs67594435	0.88[EUR][1000 genomes]
rs676586	0.83[EUR][1000 genomes]
rs67681709	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs677019	0.87[EUR][1000 genomes]
rs67734074	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67749053	0.84[ASN][1000 genomes]
rs67769616	0.88[ASN][1000 genomes]
rs67879380	0.88[ASN][1000 genomes]
rs679241	0.87[EUR][1000 genomes]
rs681321	0.81[ASN][1000 genomes]
rs687042	0.83[EUR][1000 genomes]
rs7109236	0.86[ASN][1000 genomes]
rs7115759	0.83[ASN][1000 genomes]
rs7117456	0.82[EUR][1000 genomes]
rs72643380	0.83[ASN][1000 genomes]
rs72976543	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72976568	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7814	0.93[EUR][1000 genomes]
rs7939577	0.83[ASN][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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2077408	C11orf54	cis	Esophagus Mucosa	GTEx
rs2077408	MED17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93476000-93498800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr11:93476200-93499800	Weak transcription	NH-A	brain
3	chr11:93478200-93498800	Weak transcription	Fetal Heart	heart
4	chr11:93478600-93498200	Weak transcription	Stomach Mucosa	stomach
5	chr11:93478800-93508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:93482000-93499600	Weak transcription	NHEK	skin
7	chr11:93482400-93499200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:93482800-93498400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:93483000-93497800	Strong transcription	Liver	Liver
10	chr11:93484800-93498200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:93485000-93498600	Strong transcription	Duodenum Mucosa	Duodenum
12	chr11:93485000-93499800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr11:93485200-93497600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:93485400-93498600	Strong transcription	Fetal Thymus	thymus
15	chr11:93486000-93499000	Strong transcription	Fetal Muscle Leg	muscle
16	chr11:93486600-93497800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:93486600-93498800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:93486600-93499000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:93486600-93499000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:93486600-93499000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:93486800-93497600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:93486800-93497800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr11:93486800-93497800	Strong transcription	Placenta	Placenta
24	chr11:93486800-93498000	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:93486800-93498000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr11:93486800-93498200	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:93486800-93499200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr11:93487000-93498000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:93487200-93497600	Strong transcription	Primary B cells from cord blood	blood
30	chr11:93488000-93497600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:93488200-93498200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:93488200-93498600	Strong transcription	Thymus	Thymus
33	chr11:93488200-93499200	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:93488400-93498000	Strong transcription	Left Ventricle	heart
35	chr11:93488400-93499000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr11:93488600-93497400	Strong transcription	Fetal Intestine Small	intestine
37	chr11:93488800-93498800	Weak transcription	Fetal Brain Male	brain
38	chr11:93489600-93499000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:93490200-93503200	Weak transcription	K562	blood
40	chr11:93490400-93498400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:93490400-93501400	Weak transcription	HSMM	muscle
42	chr11:93490600-93498000	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:93491000-93499800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:93492000-93498800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:93492000-93499400	Weak transcription	NHLF	lung
46	chr11:93492200-93497600	Strong transcription	Fetal Stomach	stomach
47	chr11:93492200-93498800	Strong transcription	Fetal Intestine Large	intestine
48	chr11:93492200-93499400	Weak transcription	Gastric	stomach
49	chr11:93492200-93499400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr11:93492200-93499800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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