Variant report

Variant	rs2282640
Chromosome Location	chr11:66245851-66245852
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:66245718-66248327	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr11:66245145-66248294	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:66243520-66248581	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr11:66245327-66248437	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr11:66245375-66245906	HCT-116	colon:	n/a	n/a
6	POLR2A	chr11:66245084-66248443	U87	brain:	n/a	n/a
7	POLR2A	chr11:66243706-66248342	MCF-7	breast:	n/a	n/a
8	POLR2A	chr11:66245474-66248413	K562	blood:	n/a	n/a
9	POLR2A	chr11:66245108-66248443	U87	brain:	n/a	n/a
10	POLR2A	chr11:66245461-66246277	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr11:66245805-66246304	HCT-116	colon:	n/a	n/a
12	CTCF	chr11:66245804-66247129	A549	lung:	n/a	chr11:66246572-66246590 chr11:66246574-66246587 chr11:66246008-66246029 chr11:66246006-66246024 chr11:66246578-66246587 chr11:66246567-66246588
13	POLR2A	chr11:66245842-66248441	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr11:66243528-66248662	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr11:66243707-66248130	K562	blood:	n/a	n/a
16	POLR2A	chr11:66244903-66248486	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:66245850-66248484	GM12892	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66172930..66174467-chr11:66245243..66247350,2	K562	blood:
2	chr11:66174002..66176037-chr11:66244624..66246480,2	MCF-7	breast:
3	chr11:66215751..66217886-chr11:66244738..66246507,2	K562	blood:
4	chr11:66245214..66247869-chr20:57470356..57473154,2	K562	blood:
5	chr11:66243721..66249369-chr11:66258892..66263387,7	MCF-7	breast:
6	chr11:66244873..66247008-chr11:66305651..66307290,2	K562	blood:
7	chr11:66176296..66179598-chr11:66242738..66246499,3	MCF-7	breast:
8	chr11:66245337..66248539-chr11:66443366..66447095,4	MCF-7	breast:
9	chr11:66176391..66179593-chr11:66244055..66247322,3	K562	blood:
10	chr11:66244175..66248389-chr11:66381997..66386853,5	MCF-7	breast:
11	chr11:66244850..66249884-chr11:66274125..66278778,6	MCF-7	breast:
12	chr11:66204459..66208139-chr11:66244186..66247891,5	MCF-7	breast:
13	chr11:66183845..66188748-chr11:66244741..66247932,5	MCF-7	breast:
14	chr11:66175946..66178663-chr11:66245836..66248085,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255517	TF binding region
DPP3	TF binding region
ENSG00000087460	Chromatin interaction
ENSG00000254986	Chromatin interaction
ENSG00000254510	Chromatin interaction
ENSG00000174483	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000199325	Chromatin interaction
ENSG00000256349	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000174547	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000174576	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10896126	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11110	0.93[ASW][hapmap];0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11227485	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12793712	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12795774	0.85[JPT][hapmap]
rs1785640	0.83[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2242663	0.83[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap]
rs2511220	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs2511224	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2511225	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs481296	0.85[JPT][hapmap]
rs4930376	0.83[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs55853079	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs610293	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs624561	0.85[JPT][hapmap]
rs7123875	0.94[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7947391	0.92[JPT][hapmap]
rs7951189	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][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	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
2	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
3	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
4	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active 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	74 gene(s)	inside rSNPs	diseases
6	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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 miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2282640	C11orf84	cis	parietal	SCAN
rs2282640	CDC42EP2	cis	cerebellum	SCAN
rs2282640	CCS	cis	cerebellum	SCAN
rs2282640	BBS1	cis	cerebellum	SCAN
rs2282640	UNC93B1	cis	cerebellum	SCAN
rs2282640	NDUFV1	cis	parietal	SCAN
rs2282640	SART1	cis	cerebellum	SCAN
rs2282640	SUV420H1	cis	cerebellum	SCAN
rs2282640	CTSF	cis	Esophagus Muscularis	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66235200-66246200	Weak transcription	Fetal Kidney	kidney
2	chr11:66235400-66246400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:66235400-66246600	Weak transcription	Fetal Heart	heart
4	chr11:66235400-66246600	Weak transcription	Psoas Muscle	Psoas
5	chr11:66235400-66246600	Weak transcription	HSMMtube	muscle
6	chr11:66235600-66246400	Weak transcription	A549	lung
7	chr11:66235600-66246400	Weak transcription	Hela-S3	cervix
8	chr11:66235800-66246200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr11:66235800-66246200	Weak transcription	Fetal Thymus	thymus
10	chr11:66235800-66246400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:66235800-66246400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:66235800-66246600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:66235800-66246600	Weak transcription	Primary B cells from cord blood	blood
14	chr11:66235800-66246600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr11:66235800-66246600	Weak transcription	Stomach Mucosa	stomach
16	chr11:66236000-66246200	Weak transcription	HepG2	liver
17	chr11:66236000-66246400	Weak transcription	Fetal Brain Male	brain
18	chr11:66236000-66246600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:66236000-66246600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:66236000-66246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:66236000-66246600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr11:66236200-66246200	Weak transcription	Dnd41	blood
23	chr11:66236200-66246400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:66237600-66246400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:66238000-66246200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:66240200-66246600	Weak transcription	Brain Angular Gyrus	brain
27	chr11:66240400-66246000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:66240400-66246600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr11:66240400-66246600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:66241000-66246200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:66241000-66246200	Weak transcription	Fetal Intestine Large	intestine
32	chr11:66241000-66246400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:66241400-66246200	Weak transcription	Brain Substantia Nigra	brain
34	chr11:66241600-66246000	Weak transcription	Pancreas	Pancrea
35	chr11:66241600-66246600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:66241800-66246400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr11:66241800-66246600	Weak transcription	Colonic Mucosa	Colon
38	chr11:66242000-66246200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:66242000-66246200	Weak transcription	Liver	Liver
40	chr11:66242000-66246200	Weak transcription	NHEK	skin
41	chr11:66242000-66246400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:66242000-66246400	Weak transcription	Esophagus	oesophagus
43	chr11:66242000-66246400	Weak transcription	Placenta	Placenta
44	chr11:66242000-66246400	Weak transcription	HMEC	breast
45	chr11:66242000-66246600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:66242000-66246600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr11:66242000-66246600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:66242000-66246600	Weak transcription	Fetal Lung	lung
49	chr11:66242000-66246800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:66242200-66246400	Weak transcription	Rectal Smooth Muscle	rectum

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