Variant report

Variant	rs11706542
Chromosome Location	chr3:28328583-28328584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:28328560-28328710	NB4	blood:	n/a	n/a
2	RAD21	chr3:28327959-28328593	HCT-116	colon:	n/a	n/a
3	CTCF	chr3:28328011-28328611	HCT-116	colon:	n/a	n/a
4	CTCF	chr3:28327941-28328693	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr3:28327917-28328682	A549	lung:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:27753223..27754195-chr3:28327837..28328738,6	MCF-7	breast:
2	chr3:27955406..27956542-chr3:28327800..28328748,5	MCF-7	breast:
3	chr3:28118889..28119680-chr3:28328151..28328771,2	MCF-7	breast:
4	chr3:27762979..27763746-chr3:28327989..28328770,7	MCF-7	breast:
5	chr3:28326930..28329184-chr3:28369613..28371259,2	K562	blood:
6	chr3:28309934..28311151-chr3:28327854..28329033,3	MCF-7	breast:
7	chr3:28326784..28329887-chr3:28341556..28344967,4	K562	blood:
8	chr3:28282547..28285293-chr3:28328577..28331290,2	K562	blood:
9	chr3:27753666..27754216-chr3:28328074..28328762,2	MCF-7	breast:
10	chr3:28324669..28327631-chr3:28328520..28331912,3	K562	blood:
11	chr3:28327412..28329270-chr3:28333865..28335490,2	K562	blood:

No data

Variant related genes	Relation type
CMC1	TF binding region
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11706332	0.87[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs11707705	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs11720107	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs11918050	0.90[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs11921692	0.91[CEU][hapmap];0.92[CHB][hapmap]
rs11921943	0.92[CHB][hapmap]
rs12107256	0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap]
rs13075840	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs13081520	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs13082167	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs13083544	0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap]
rs13085075	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs13087143	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs13087774	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs13088574	0.91[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap]
rs13090296	0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs13090439	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs13093242	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs13095628	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs13095675	0.92[CHB][hapmap]
rs1457910	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap]
rs1585211	0.92[CHB][hapmap]
rs1598846	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs1599826	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs1606386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1606388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs1610238	0.92[CHB][hapmap];0.84[MEX][hapmap]
rs17021221	0.92[CHB][hapmap]
rs17021306	0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs17021402	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs17357206	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap]
rs17638742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs17638991	0.87[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs17639978	0.86[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs17695765	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap]
rs17695884	0.87[CEU][hapmap];0.92[CHB][hapmap]
rs17696025	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap]
rs17696459	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs1870259	0.92[CHB][hapmap]
rs2168799	0.92[CHB][hapmap]
rs36105900	0.91[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap]
rs3762797	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4452283	0.86[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap]
rs4680909	0.92[CHB][hapmap]
rs4680913	0.92[CHB][hapmap]
rs6771057	0.92[CHB][hapmap]
rs6771460	0.87[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap]
rs6803692	0.92[CHB][hapmap]
rs7434193	0.84[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap]
rs7639750	0.92[CHB][hapmap]
rs7641491	0.92[CHB][hapmap];0.85[CHD][hapmap]
rs7649498	0.92[CHB][hapmap]
rs7651883	0.92[CHB][hapmap]
rs952888	1.00[CEU][hapmap]
rs9843464	0.92[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv1420005	chr3:28328583-28328584	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11706542	SSTR2	trans	brain	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28303600-28340600	Weak transcription	NHEK	skin
2	chr3:28304200-28332400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:28306400-28332400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:28306600-28335800	Weak transcription	Hela-S3	cervix
5	chr3:28309000-28336600	Weak transcription	HUVEC	blood vessel
6	chr3:28314200-28332400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:28314400-28332400	Weak transcription	Ovary	ovary
8	chr3:28314400-28365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:28314600-28332600	Weak transcription	Left Ventricle	heart
10	chr3:28314800-28343400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:28315000-28332400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:28315000-28333000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:28315000-28363000	Weak transcription	A549	lung
14	chr3:28315200-28332200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:28315600-28332400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:28315600-28332400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:28315600-28332400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:28315800-28332200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:28315800-28332200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:28315800-28332400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:28316000-28332000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:28316200-28333200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:28316400-28332000	Weak transcription	K562	blood
24	chr3:28317200-28332200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:28317400-28332000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:28317400-28332400	Weak transcription	HSMM	muscle
27	chr3:28317400-28337200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:28317600-28331800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:28317600-28331800	Weak transcription	GM12878-XiMat	blood
30	chr3:28317600-28332200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:28317600-28332400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:28317600-28332400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:28317600-28332400	Weak transcription	Lung	lung
34	chr3:28317600-28332400	Weak transcription	Thymus	Thymus
35	chr3:28317600-28337000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:28317600-28337000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:28317600-28337200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:28317600-28337600	Weak transcription	Fetal Intestine Large	intestine
39	chr3:28317600-28341200	Weak transcription	Fetal Thymus	thymus
40	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
42	chr3:28317800-28331800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:28317800-28332400	Weak transcription	Fetal Stomach	stomach
44	chr3:28317800-28332400	Weak transcription	Right Ventricle	heart
45	chr3:28317800-28337200	Weak transcription	Fetal Intestine Small	intestine
46	chr3:28317800-28343000	Weak transcription	HepG2	liver
47	chr3:28318600-28332200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:28319600-28331800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:28320800-28331800	Weak transcription	Primary B cells from cord blood	blood
50	chr3:28321800-28332200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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