Variant report

Variant	rs11228271
Chromosome Location	chr11:68299226-68299227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr11:68299090-68299322	T-47D	breast:	n/a	n/a
2	FOXA1	chr11:68299014-68299356	T-47D	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:68296455..68299790-chr11:68302079..68305805,5	MCF-7	breast:
2	chr11:68298372..68300264-chr11:68312543..68314090,2	MCF-7	breast:
3	chr11:68294325..68295955-chr11:68298713..68301491,2	MCF-7	breast:
4	chr11:68295776..68299439-chr11:68303411..68307238,4	MCF-7	breast:
5	chr11:68297338..68300739-chr11:68302281..68305792,3	K562	blood:
6	chr11:68294569..68300884-chr11:68301250..68310355,12	K562	blood:

No data

Variant related genes	Relation type
PPP6R3	TF binding region
ENSG00000110075	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11228270	1.00[YRI][hapmap]
rs11228296	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11228297	0.84[EUR][1000 genomes]
rs11512724	0.84[EUR][1000 genomes]
rs12363572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs1996	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2242340	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2510375	1.00[MEX][hapmap]
rs3781579	1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs3781596	1.00[ASW][hapmap]
rs7123591	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs729635	1.00[ASW][hapmap]
rs73504493	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73516825	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036561	chr11:68123135-68315685	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv1792339	chr11:68199008-68299226	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv1803199	chr11:68199008-68299226	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv1842405	chr11:68199008-68299226	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3431317	chr11:68282676-68411867	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	esv3478641	chr11:68282679-68411856	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	esv3478652	chr11:68282679-68411856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	esv3425206	chr11:68282708-68411817	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	esv3511614	chr11:68282726-68411806	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	esv3511615	chr11:68282726-68411806	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
11	esv3348204	chr11:68282891-68411839	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv832195	chr11:68286383-68474611	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv430403	chr11:68297201-68448324	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11228271	FOSL1	cis	cerebellum	SCAN
rs11228271	C11orf59	cis	parietal	SCAN
rs11228271	SHANK2	cis	cerebellum	SCAN
rs11228271	AIP	cis	cerebellum	SCAN
rs11228271	C11orf85	cis	parietal	SCAN
rs11228271	SPTBN2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:68265200-68302600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:68268600-68303800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:68276000-68305600	Weak transcription	Fetal Brain Male	brain
4	chr11:68276600-68304000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:68277600-68336000	Strong transcription	Dnd41	blood
6	chr11:68283000-68358200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:68286200-68300200	Strong transcription	Hela-S3	cervix
8	chr11:68286400-68303200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:68287200-68301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:68288600-68309000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:68292600-68301400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:68292600-68308200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:68293200-68302200	Weak transcription	Brain Substantia Nigra	brain
14	chr11:68293600-68299800	Strong transcription	NHEK	skin
15	chr11:68293600-68300000	Strong transcription	A549	lung
16	chr11:68295000-68301400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:68295400-68300600	Weak transcription	Colonic Mucosa	Colon
18	chr11:68295400-68300600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:68295400-68301400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:68295400-68305200	Weak transcription	HMEC	breast
21	chr11:68295400-68306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:68295600-68300200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr11:68295600-68302600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:68295600-68305600	Weak transcription	Fetal Brain Female	brain
25	chr11:68295800-68306200	Weak transcription	HSMMtube	muscle
26	chr11:68296200-68302600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr11:68296400-68300000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:68296400-68300000	Weak transcription	HSMM	muscle
29	chr11:68296400-68301000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr11:68296400-68301200	Weak transcription	Pancreas	Pancrea
31	chr11:68296400-68302600	Weak transcription	Esophagus	oesophagus
32	chr11:68296400-68305400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:68296400-68306000	Weak transcription	Fetal Heart	heart
34	chr11:68296400-68307800	Strong transcription	GM12878-XiMat	blood
35	chr11:68296600-68299400	Weak transcription	NHDF-Ad	bronchial
36	chr11:68296600-68299600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr11:68296600-68299600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr11:68296600-68299800	Weak transcription	Liver	Liver
39	chr11:68296600-68299800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr11:68296600-68300000	Weak transcription	Adipose Nuclei	Adipose
41	chr11:68296600-68300400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:68296600-68300400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:68296600-68300600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:68296600-68300600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:68296600-68300600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:68296600-68300800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr11:68296600-68301200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:68296600-68301200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:68296600-68301200	Weak transcription	Right Atrium	heart
50	chr11:68296600-68301400	Weak transcription	H1 Cell Line	embryonic stem cell

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