Variant report

Variant	rs11211342
Chromosome Location	chr1:47163098-47163099
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	CEBPB	chr1:47162787-47163129	IMR90	lung:	n/a	chr1:47162951-47162968 chr1:47162952-47162965

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47160988..47163658-chr1:47182412..47184770,2	MCF-7	breast:

Variant related genes	Relation type
EFCAB14	TF binding region
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10749863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749864	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473292	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1545206	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595898	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1816730	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs1866770	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099766	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165317	1.00[YRI][hapmap]
rs2218191	0.94[EUR][1000 genomes]
rs2476158	0.92[EUR][1000 genomes]
rs35050319	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35861275	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4097354	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4553120	1.00[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]
rs4660359	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4660954	1.00[YRI][hapmap]
rs4660956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618505	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6668899	0.84[ASN][1000 genomes]
rs7516616	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893954	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription 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	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11211342	EFCAB14	cis	Esophagus Mucosa	GTEx
rs11211342	EFCAB14	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47155600-47169000	Weak transcription	Stomach Mucosa	stomach
5	chr1:47157600-47172200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:47158200-47172000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:47158800-47171000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:47159400-47171200	Weak transcription	Right Ventricle	heart
10	chr1:47159400-47172200	Weak transcription	Psoas Muscle	Psoas
11	chr1:47159600-47168200	Weak transcription	HMEC	breast
12	chr1:47160600-47165000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:47160600-47165200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:47160600-47165200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:47160600-47165800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:47160600-47169000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:47160600-47169400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:47160600-47173600	Strong transcription	Primary T cells from cord blood	blood
19	chr1:47160600-47174000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:47160600-47181200	Strong transcription	Dnd41	blood
21	chr1:47160800-47163200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:47160800-47163200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:47160800-47163400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:47160800-47163400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:47160800-47163400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:47160800-47163400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:47160800-47163400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:47160800-47163400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:47160800-47163400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:47160800-47163400	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:47160800-47163400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr1:47160800-47163600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:47160800-47163600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr1:47160800-47163800	Strong transcription	Fetal Intestine Large	intestine
35	chr1:47160800-47164000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:47160800-47164600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:47160800-47164800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:47160800-47164800	Strong transcription	Adipose Nuclei	Adipose
39	chr1:47160800-47165000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:47160800-47165000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:47160800-47165200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:47160800-47165200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:47160800-47165600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:47160800-47165600	Strong transcription	Fetal Thymus	thymus
45	chr1:47160800-47165600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:47160800-47166000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:47160800-47166000	Strong transcription	Fetal Muscle Leg	muscle
48	chr1:47160800-47166000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:47160800-47166200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:47160800-47166600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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