Variant report

Variant	rs360140
Chromosome Location	chr11:9776567-9776568
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr11:9776161-9776642	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:9776527-9782028	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr11:9776291-9778152	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:9776442-9776658	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:9775557-9779107	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr11:9776500-9776650	GM12873	blood:	n/a	n/a
7	POLR2A	chr11:9775144-9782147	PANC-1	pancreas:	n/a	n/a
8	PML	chr11:9776064-9776614	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:9775224-9778035	GM12892	blood:	n/a	n/a
10	POLR2A	chr11:9776225-9777710	GM12892	blood:	n/a	n/a
11	POLR2A	chr11:9775330-9778222	GM12891	blood:	n/a	n/a
12	POLR2A	chr11:9776155-9776763	GM12892	blood:	n/a	n/a
13	POLR2A	chr11:9776227-9776689	HUVEC	blood vessel:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9775646..9777707-chr11:9778312..9780698,2	MCF-7	breast:
2	chr11:9774053..9775652-chr11:9775984..9777697,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SBF2-2	chr11:9776317-9778445	ENSG00000245522
2	lnc-SBF2-2	chr11:9776104-9777930	XLOC_009371

No data

Variant related genes	Relation type
SBF2-AS1	TF binding region
ENSG00000246273	Chromatin interaction
ENSG00000245522	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10118	0.84[JPT][hapmap]
rs10770059	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10770062	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs183110	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap]
rs2173030	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs2645029	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs360120	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360124	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360129	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360141	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs360142	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360143	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360150	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360151	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs360155	0.91[ASN][1000 genomes]
rs360158	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs380806	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs415895	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs432849	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs436637	0.83[EUR][1000 genomes]
rs438151	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs446760	0.85[CHB][hapmap]
rs472487	0.85[JPT][hapmap]
rs4910498	0.90[EUR][1000 genomes]
rs4910499	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs634680	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs6483656	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6483726	0.80[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs360140	MRVI1	cis	parietal	SCAN
rs360140	NRIP3	cis	parietal	SCAN
rs360140	NM_015055	cis	multi-tissue	Pritchard
rs360140	AF075116	cis	multi-tissue	Pritchard
rs360140	ASCL3	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9742200-9779400	Weak transcription	Fetal Brain Male	brain
2	chr11:9755000-9777600	Weak transcription	Colonic Mucosa	Colon
3	chr11:9761000-9777200	Weak transcription	Fetal Kidney	kidney
4	chr11:9762400-9777200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:9762400-9777400	Weak transcription	Esophagus	oesophagus
6	chr11:9762400-9777400	Weak transcription	Right Ventricle	heart
7	chr11:9762400-9779400	Weak transcription	Liver	Liver
8	chr11:9762400-9779400	Weak transcription	Psoas Muscle	Psoas
9	chr11:9762600-9779200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr11:9762800-9779400	Weak transcription	Fetal Brain Female	brain
11	chr11:9763600-9779400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:9770200-9777000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:9770200-9777000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:9770200-9777600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr11:9770200-9777600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:9770200-9779200	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:9770200-9779400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:9770200-9779400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:9770200-9779400	Weak transcription	Ovary	ovary
20	chr11:9770200-9779400	Weak transcription	Pancreas	Pancrea
21	chr11:9770200-9779600	Weak transcription	Small Intestine	intestine
22	chr11:9770400-9776600	Weak transcription	Fetal Thymus	thymus
23	chr11:9770400-9777000	Weak transcription	Fetal Lung	lung
24	chr11:9770400-9779200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:9770400-9779400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:9770600-9777400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:9772400-9777000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:9772400-9777200	Weak transcription	Fetal Stomach	stomach
29	chr11:9772400-9777200	Weak transcription	Spleen	Spleen
30	chr11:9772400-9779200	Weak transcription	Primary T cells from cord blood	blood
31	chr11:9772400-9779400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:9772400-9779400	Weak transcription	Gastric	stomach
33	chr11:9772600-9777000	Weak transcription	Left Ventricle	heart
34	chr11:9772600-9777200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr11:9772600-9777200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr11:9772800-9776800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:9772800-9777000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:9773400-9776600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:9773800-9777000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:9773800-9778200	Enhancers	NH-A	brain
41	chr11:9773800-9779000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr11:9773800-9779400	Enhancers	HMEC	breast
43	chr11:9773800-9779800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:9774000-9777000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:9774000-9777200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:9774000-9777400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:9774000-9777400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr11:9774000-9777400	Weak transcription	Lung	lung
49	chr11:9774000-9778200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:9774000-9778200	Enhancers	Osteobl	bone

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