Variant report

Variant	rs679241
Chromosome Location	chr11:93551914-93551915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:93549611..93555766-chr11:93556424..93562226,8	K562	blood:
2	chr11:93535225..93537724-chr11:93550951..93552669,2	MCF-7	breast:
3	chr11:93461936..93464085-chr11:93550209..93551973,2	K562	blood:
4	chr11:93551501..93553047-chr11:93554651..93556227,2	K562	blood:

Variant related genes	Relation type
ENSG00000207112	Chromatin interaction
ENSG00000206911	Chromatin interaction
ENSG00000214376	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10765635	0.90[ASN][1000 genomes]
rs11020532	0.92[ASN][1000 genomes]
rs1150326	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1298531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16919444	0.93[ASN][1000 genomes]
rs2077408	0.87[EUR][1000 genomes]
rs34057693	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3763808	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55734929	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58063272	0.93[ASN][1000 genomes]
rs584084	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs58976781	0.93[ASN][1000 genomes]
rs59726694	0.92[ASN][1000 genomes]
rs598495	0.93[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs601792	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs606087	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs61498836	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs615428	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61904953	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61904957	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61906576	0.99[ASN][1000 genomes]
rs61906579	0.96[ASN][1000 genomes]
rs625685	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs626216	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs628665	0.96[EUR][1000 genomes]
rs636482	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs654896	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs664257	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66460850	0.87[EUR][1000 genomes]
rs66483735	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66487029	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666074	0.84[AMR][1000 genomes]
rs66760087	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66797025	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66887806	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs669565	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66963387	0.93[ASN][1000 genomes]
rs670391	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs674886	0.92[EUR][1000 genomes]
rs67594435	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676586	0.86[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs67681709	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs677019	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67734074	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs687042	0.96[EUR][1000 genomes]
rs687507	0.86[CEU][hapmap];0.85[AMR][1000 genomes]
rs7103466	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7114611	0.96[ASN][1000 genomes]
rs7115115	0.96[ASN][1000 genomes]
rs7119738	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7125525	0.96[ASN][1000 genomes]
rs7125919	0.93[ASN][1000 genomes]
rs7126745	0.96[ASN][1000 genomes]
rs7129970	0.93[ASN][1000 genomes]
rs72976543	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72976568	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7814	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7924366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs679241	C11orf54	cis	parietal	SCAN
rs679241	MED17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93533000-93555600	Weak transcription	Small Intestine	intestine
2	chr11:93543000-93552200	Weak transcription	Esophagus	oesophagus
3	chr11:93543000-93553200	Weak transcription	Aorta	Aorta
4	chr11:93543000-93554400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:93544600-93552800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:93546200-93552200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:93546200-93553200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:93546400-93553000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:93546400-93553600	Weak transcription	HepG2	liver
10	chr11:93546400-93554200	Weak transcription	Colonic Mucosa	Colon
11	chr11:93546400-93566200	Weak transcription	Brain Angular Gyrus	brain
12	chr11:93546600-93552400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:93546600-93554200	Weak transcription	K562	blood
14	chr11:93547400-93553400	Weak transcription	Ovary	ovary
15	chr11:93547600-93552200	Weak transcription	NHEK	skin
16	chr11:93547800-93552800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:93547800-93553600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr11:93547800-93553600	Weak transcription	HSMMtube	muscle
19	chr11:93547800-93554200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:93547800-93554400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:93548000-93552600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:93548000-93555800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:93548200-93552000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:93548200-93552800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:93548200-93553600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:93548400-93552000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:93548400-93552400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:93548400-93553600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr11:93548400-93554200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:93548600-93552200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr11:93548800-93553200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:93549000-93552200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:93549000-93552400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:93549000-93553400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr11:93549200-93552000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr11:93549200-93552000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:93549200-93552000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr11:93549200-93552200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:93549200-93552200	Weak transcription	Fetal Thymus	thymus
40	chr11:93549200-93552400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:93549200-93552800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:93549200-93552800	Weak transcription	Fetal Intestine Large	intestine
43	chr11:93549200-93552800	Weak transcription	Lung	lung
44	chr11:93549200-93553200	Weak transcription	GM12878-XiMat	blood
45	chr11:93549200-93553600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr11:93549200-93553600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr11:93549200-93553600	Weak transcription	Brain Substantia Nigra	brain
48	chr11:93549200-93553800	Weak transcription	HSMM	muscle
49	chr11:93549200-93554400	Weak transcription	Brain Anterior Caudate	brain
50	chr11:93549200-93554600	Weak transcription	Placenta	Placenta

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