Variant report

Variant	rs555826
Chromosome Location	chr11:66040053-66040054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66040044-66040623	K562	blood:	n/a	n/a
2	POLR2A	chr11:66039776-66040416	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66038976..66041430-chr11:66054512..66056823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254762	TF binding region
ENSG00000174851	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1151532	0.85[AFR][1000 genomes]
rs11544832	1.00[CHD][hapmap]
rs11823756	1.00[CHD][hapmap]
rs11825510	1.00[CHD][hapmap]
rs1190945	0.92[AFR][1000 genomes]
rs1190946	0.86[AFR][1000 genomes]
rs1191715	0.81[AFR][1000 genomes]
rs1203551	0.92[AFR][1000 genomes]
rs1203552	0.92[AFR][1000 genomes]
rs1203749	0.85[AFR][1000 genomes]
rs1203750	0.85[AFR][1000 genomes]
rs1203801	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1630638	0.81[AFR][1000 genomes]
rs1783732	1.00[YRI][hapmap]
rs2452687	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3016315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3017606	0.89[AFR][1000 genomes]
rs471203	1.00[MEX][hapmap]
rs471709	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs472853	0.85[AFR][1000 genomes]
rs475817	0.85[AFR][1000 genomes]
rs477001	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4930332	0.82[AFR][1000 genomes]
rs504456	0.85[AFR][1000 genomes]
rs505412	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs505642	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs510398	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs512316	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs515778	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs519911	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs527279	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs541954	1.00[YRI][hapmap]
rs547282	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs547892	0.85[AFR][1000 genomes]
rs549228	0.85[AFR][1000 genomes]
rs551652	0.85[AFR][1000 genomes]
rs555527	1.00[YRI][hapmap]
rs559298	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs560105	0.85[AFR][1000 genomes]
rs561199	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs561869	0.85[AFR][1000 genomes]
rs567414	0.85[AFR][1000 genomes]
rs568423	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs571368	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs572697	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs577301	0.85[AFR][1000 genomes]
rs581247	0.92[AFR][1000 genomes]
rs693382	0.85[AFR][1000 genomes]
rs7110351	1.00[CHD][hapmap]
rs7947668	0.81[AFR][1000 genomes]
rs948358	0.82[ASW][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs948477	0.81[AFR][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	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
5	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs555826	LOC404266	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66037400-66044600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:66037400-66044800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:66037600-66043600	Strong transcription	Osteobl	bone
4	chr11:66037600-66044600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:66037600-66045000	Genic enhancers	Fetal Thymus	thymus
6	chr11:66037800-66044000	Strong transcription	NHEK	skin
7	chr11:66037800-66044200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:66037800-66044600	Strong transcription	Fetal Intestine Small	intestine
9	chr11:66037800-66044800	Strong transcription	Fetal Stomach	stomach
10	chr11:66038000-66040200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
11	chr11:66038000-66042600	Strong transcription	A549	lung
12	chr11:66038000-66042800	Strong transcription	K562	blood
13	chr11:66038000-66043000	Genic enhancers	Primary T cells fromperipheralblood	blood
14	chr11:66038000-66043200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:66038000-66043600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:66038000-66044200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:66038000-66044200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:66038000-66044200	Strong transcription	Brain Cingulate Gyrus	brain
19	chr11:66038000-66044200	Strong transcription	Fetal Intestine Large	intestine
20	chr11:66038000-66044200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr11:66038000-66044200	Strong transcription	NHLF	lung
22	chr11:66038000-66044600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:66038000-66044600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:66038000-66044800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:66038200-66041800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr11:66038200-66042400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:66038200-66042800	Strong transcription	Fetal Lung	lung
28	chr11:66038200-66043600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:66038200-66043800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:66038200-66044200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:66038200-66044200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr11:66038200-66044200	Strong transcription	Colonic Mucosa	Colon
33	chr11:66038200-66044200	Strong transcription	Lung	lung
34	chr11:66038200-66044200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr11:66038200-66044600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:66038200-66045000	Weak transcription	Right Atrium	heart
37	chr11:66038400-66040200	Strong transcription	Fetal Muscle Leg	muscle
38	chr11:66038400-66040600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
39	chr11:66038400-66041600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:66038400-66041600	Strong transcription	Thymus	Thymus
41	chr11:66038400-66044000	Strong transcription	Brain Anterior Caudate	brain
42	chr11:66038400-66044400	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr11:66038400-66044800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:66038400-66045000	Weak transcription	Fetal Heart	heart
45	chr11:66038400-66045000	Strong transcription	Gastric	stomach
46	chr11:66038400-66045200	Weak transcription	Psoas Muscle	Psoas
47	chr11:66038600-66040200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr11:66038600-66040600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:66038600-66044000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:66038600-66044000	Strong transcription	Duodenum Mucosa	Duodenum

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