Variant report

Variant	rs2077432
Chromosome Location	chr11:66621383-66621384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66621296-66622108	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66620817..66623976-chr11:66646170..66651314,5	MCF-7	breast:
2	chr11:66620776..66623722-chr11:66770531..66772844,2	K562	blood:
3	chr11:66434007..66436161-chr11:66621311..66623871,2	MCF-7	breast:
4	chr11:66441690..66444071-chr11:66620456..66623383,2	K562	blood:
5	chr11:66382895..66384620-chr11:66621136..66623710,2	MCF-7	breast:

No data

Variant related genes	Relation type
LRFN4	TF binding region
PC	TF binding region
ENSG00000173914	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000258297	Chromatin interaction
ENSG00000239306	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10160758	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10750790	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10791889	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs10791892	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10896135	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10896139	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11227610	0.87[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11600959	0.90[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2167457	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2187041	0.95[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs2380760	0.87[EUR][1000 genomes]
rs3741194	0.95[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3741364	0.83[GIH][hapmap]
rs4008953	0.89[EUR][1000 genomes]
rs4576826	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4930184	0.83[EUR][1000 genomes]
rs4930390	1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs551708	0.82[CEU][hapmap]
rs6591222	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7103627	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7119426	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7120256	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7122539	0.83[TSI][hapmap]
rs714766	0.86[EUR][1000 genomes]
rs7570	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7930203	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7948839	0.90[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9971487	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2077432	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs2077432	RARRES3	cis	parietal	SCAN
rs2077432	C11orf80	cis	cerebellum	SCAN
rs2077432	B3GNT1	cis	parietal	SCAN
rs2077432	EHBP1L1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66612000-66623000	Weak transcription	Psoas Muscle	Psoas
2	chr11:66612000-66623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:66612000-66623200	Weak transcription	Right Atrium	heart
4	chr11:66612200-66623000	Weak transcription	Fetal Kidney	kidney
5	chr11:66612200-66623000	Weak transcription	Stomach Mucosa	stomach
6	chr11:66612200-66623000	Weak transcription	HSMM	muscle
7	chr11:66612200-66623200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:66612200-66623200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:66612400-66623200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:66612400-66623200	Weak transcription	NH-A	brain
11	chr11:66612800-66623200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:66613200-66622400	Weak transcription	Fetal Brain Male	brain
13	chr11:66613400-66623000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:66614200-66622400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:66614400-66623000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:66614400-66623000	Weak transcription	Osteobl	bone
17	chr11:66614600-66622800	Weak transcription	Fetal Lung	lung
18	chr11:66614600-66623000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:66614600-66623000	Weak transcription	HUVEC	blood vessel
20	chr11:66614800-66622000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:66615200-66622000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:66615200-66623000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:66615400-66623000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:66615400-66623000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:66615400-66623000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:66615600-66621800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:66615600-66622800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:66615600-66623000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:66615600-66623200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:66615800-66622400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:66615800-66622800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:66615800-66622800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:66615800-66622800	Weak transcription	Left Ventricle	heart
34	chr11:66615800-66623000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr11:66616000-66623000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr11:66616000-66623000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr11:66616200-66623000	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:66616200-66623200	Weak transcription	Colonic Mucosa	Colon
39	chr11:66616400-66623000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr11:66616400-66623200	Weak transcription	Aorta	Aorta
41	chr11:66616400-66623200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr11:66616600-66622800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:66616600-66622800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr11:66616600-66622800	Weak transcription	HSMMtube	muscle
45	chr11:66616600-66623000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr11:66616600-66623000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr11:66616600-66623000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:66616600-66623200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:66616600-66623200	Weak transcription	NHDF-Ad	bronchial
50	chr11:66616800-66622800	Weak transcription	Muscle Satellite Cultured Cells	--

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