Variant report

Variant	rs622779
Chromosome Location	chr11:65744247-65744248
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	chr11:65743159-65744862	K562	blood:	n/a	n/a
2	POLR2A	chr11:65743394-65744368	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:65744097-65744248	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:65743527-65744800	HL-60	blood:	n/a	n/a
5	POLR2A	chr11:65742864-65745188	GM12891	blood:	n/a	n/a
6	POLR2A	chr11:65743675-65744736	K562	blood:	n/a	n/a
7	POLR2A	chr11:65743234-65744303	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:65744221-65744934	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:65744160-65744426	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr11:65742494-65745636	GM12878	blood:	n/a	n/a
11	POLR2A	chr11:65743049-65745415	GM12892	blood:	n/a	n/a
12	POLR2A	chr11:65743940-65745194	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr11:65743069-65745339	GM12892	blood:	n/a	n/a
14	POLR2A	chr11:65744188-65744668	HL-60	blood:	n/a	n/a
15	ZNF263	chr11:65743976-65744339	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65742158..65748813-chr11:65749011..65756801,11	MCF-7	breast:
2	chr11:65729174..65730832-chr11:65742979..65745166,3	MCF-7	breast:

Variant related genes	Relation type
SART1	TF binding region
ENSG00000254867	Chromatin interaction
ENSG00000175467	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1151510	1.00[EUR][1000 genomes]
rs1151511	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs1151514	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];1.00[EUR][1000 genomes]
rs1191716	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1192184	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1204011	1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1786172	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1786174	0.83[EUR][1000 genomes]
rs502363	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];1.00[EUR][1000 genomes]
rs506873	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs507672	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs522553	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs534201	0.99[EUR][1000 genomes]
rs540584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs543952	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs548435	0.83[EUR][1000 genomes]
rs548495	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs549334	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs586921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610497	0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs615646	1.00[EUR][1000 genomes]
rs616073	0.87[EUR][1000 genomes]
rs619701	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs632640	0.83[EUR][1000 genomes]
rs645571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs668210	0.85[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs677350	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs684546	0.85[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs688862	0.97[LWK][hapmap];0.90[YRI][hapmap]
rs7933510	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
3	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
7	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS 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	56 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs622779	SNX32	cis	parietal	SCAN
rs622779	SNORD26	cis	parietal	SCAN
rs622779	SCGB1D1	cis	cerebellum	SCAN
rs622779	DKFZp761E198	cis	cerebellum	SCAN
rs622779	RAD9A	cis	cerebellum	SCAN
rs622779	RTN3	cis	parietal	SCAN
rs622779	PCNXL3	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65729800-65746200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65730600-65767800	Weak transcription	Right Atrium	heart
3	chr11:65731000-65744600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:65731200-65747400	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr11:65731200-65747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:65731200-65748600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr11:65731200-65749600	Strong transcription	Fetal Intestine Small	intestine
8	chr11:65731400-65747600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr11:65731400-65747600	Strong transcription	Fetal Thymus	thymus
10	chr11:65731400-65748000	Strong transcription	Thymus	Thymus
11	chr11:65731600-65747400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:65731600-65747800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:65731800-65749000	Strong transcription	Fetal Stomach	stomach
14	chr11:65732000-65747200	Strong transcription	Lung	lung
15	chr11:65732400-65748800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr11:65732800-65748200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:65735200-65750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:65735800-65756600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr11:65736400-65767400	Weak transcription	Psoas Muscle	Psoas
20	chr11:65736800-65744400	Weak transcription	HepG2	liver
21	chr11:65736800-65745000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:65736800-65747800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr11:65737000-65748000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:65737200-65747800	Strong transcription	Placenta	Placenta
25	chr11:65737200-65747800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:65737600-65744800	Weak transcription	Small Intestine	intestine
27	chr11:65737600-65748000	Strong transcription	Fetal Muscle Leg	muscle
28	chr11:65737800-65744600	Weak transcription	HUVEC	blood vessel
29	chr11:65737800-65756600	Weak transcription	Stomach Mucosa	stomach
30	chr11:65738200-65744600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:65738200-65744800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:65739000-65747800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:65739200-65749600	Strong transcription	Fetal Brain Female	brain
34	chr11:65739400-65747200	Strong transcription	Brain Hippocampus Middle	brain
35	chr11:65739400-65747400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr11:65739600-65748000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:65739600-65748800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:65739600-65756400	Weak transcription	Fetal Kidney	kidney
39	chr11:65739800-65747600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:65739800-65756400	Weak transcription	Hela-S3	cervix
41	chr11:65740000-65747200	Strong transcription	Spleen	Spleen
42	chr11:65740600-65748000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:65740800-65745400	Strong transcription	Rectal Smooth Muscle	rectum
44	chr11:65740800-65745600	Strong transcription	Fetal Lung	lung
45	chr11:65740800-65748000	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr11:65741000-65746800	Strong transcription	Brain Substantia Nigra	brain
47	chr11:65741000-65747800	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr11:65741200-65765000	Weak transcription	NHDF-Ad	bronchial
49	chr11:65741400-65744600	Weak transcription	GM12878-XiMat	blood
50	chr11:65741400-65762000	Weak transcription	HSMMtube	muscle

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