Variant report

Variant	rs2256154
Chromosome Location	chr11:67090571-67090572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:67088208..67091047-chr11:67138396..67140194,2	MCF-7	breast:
2	chr11:67087147..67090755-chr11:67140887..67143094,4	MCF-7	breast:
3	chr11:67088729..67091656-chr11:67105990..67108067,2	K562	blood:
4	chr11:67088738..67091729-chr11:67113065..67116327,3	MCF-7	breast:
5	chr11:67032012..67034132-chr11:67089605..67092011,2	K562	blood:
6	chr11:67076937..67081863-chr11:67086712..67091272,5	K562	blood:
7	chr11:67083205..67091159-chr11:67142322..67150295,9	MCF-7	breast:
8	chr11:67089180..67091278-chr11:67103775..67106325,2	MCF-7	breast:
9	chr11:67088738..67090826-chr11:67092004..67094018,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173020	Chromatin interaction
ENSG00000172830	Chromatin interaction
ENSG00000256514	Chromatin interaction
ENSG00000175505	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10896167	0.95[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10896168	0.84[ASN][1000 genomes]
rs10896169	0.82[ASN][1000 genomes]
rs11227756	0.92[CHD][hapmap]
rs11601700	0.84[ASN][1000 genomes]
rs12290164	0.86[JPT][hapmap]
rs12788752	0.92[CHD][hapmap];0.93[JPT][hapmap]
rs1540135	0.83[ASN][1000 genomes]
rs1558256	0.95[CHD][hapmap];0.86[JPT][hapmap]
rs1626067	0.87[GIH][hapmap];0.96[MEX][hapmap]
rs1638566	0.95[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs1638567	0.95[CHD][hapmap];0.93[JPT][hapmap]
rs1638571	0.95[CHD][hapmap];0.93[JPT][hapmap]
rs1638574	0.84[ASN][1000 genomes]
rs1790740	0.95[CHD][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2066496	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2071007	0.92[CHD][hapmap]
rs2276118	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2286620	0.82[CHD][hapmap]
rs2429460	0.82[ASN][1000 genomes]
rs2429462	0.87[ASN][1000 genomes]
rs2514256	0.95[CHD][hapmap];0.93[JPT][hapmap]
rs2514258	0.82[ASN][1000 genomes]
rs3758943	0.92[JPT][hapmap]
rs3781941	0.95[CHD][hapmap];0.93[JPT][hapmap]
rs3781942	0.95[CHD][hapmap];0.93[JPT][hapmap]
rs3781943	0.92[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4255546	0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4375446	0.92[CHD][hapmap]
rs4542419	0.92[CHD][hapmap]
rs4930192	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs4930197	0.95[CHD][hapmap];0.92[JPT][hapmap]
rs4930418	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs674499	0.86[CHD][hapmap]
rs7106352	0.84[ASN][1000 genomes]
rs7480390	0.93[JPT][hapmap]
rs872110	0.95[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv933183	chr11:67008447-67160993	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv897796	chr11:67021518-67186000	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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 miRNA target site	206 gene(s)	inside rSNPs	diseases
5	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv468603	chr11:67033076-67164495	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
7	nsv555253	chr11:67033076-67164495	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
9	nsv1047890	chr11:67058231-67184436	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv1048230	chr11:67058231-67252397	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
11	nsv897804	chr11:67090571-67224278	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2256154	TMEM134	cis	cerebellum	SCAN
rs2256154	PTPRCAP	cis	Adipose Subcutaneous	GTEx
rs2256154	RPS6KB2	cis	lymphoblastoid	seeQTL
rs2256154	PYGM	cis	parietal	SCAN
rs2256154	SSH3	cis	cerebellum	SCAN
rs2256154	GSTP1	cis	brain	BrainEAC
rs2256154	GSTP1	cis	cerebellum	SCAN
rs2256154	RPS6KB2	cis	multi-tissue	Pritchard
rs2256154	PTPRCAP	cis	Skin Sun Exposed Lower leg	GTEx
rs2256154	CPT1A	cis	cerebellum	SCAN
rs2256154	HRASLS5	cis	cerebellum	SCAN
rs2256154	GSTP1	cis	parietal	SCAN
rs2256154	PTPRCAP	cis	parietal	SCAN
rs2256154	LRFN4	cis	cerebellum	SCAN
rs2256154	CATSPER1	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67086000-67090800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:67086000-67104400	Weak transcription	Aorta	Aorta
3	chr11:67086200-67092200	Weak transcription	HSMMtube	muscle
4	chr11:67086200-67097400	Weak transcription	Primary T cells from cord blood	blood
5	chr11:67086200-67101400	Weak transcription	Colonic Mucosa	Colon
6	chr11:67086200-67113600	Weak transcription	Osteobl	bone
7	chr11:67086400-67098000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:67086400-67100400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:67086400-67102800	Weak transcription	Liver	Liver
10	chr11:67086400-67104000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:67086400-67110200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr11:67086400-67111200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:67086400-67111600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr11:67086400-67112600	Weak transcription	Fetal Lung	lung
15	chr11:67086400-67120000	Weak transcription	Brain Germinal Matrix	brain
16	chr11:67086600-67091000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:67086600-67091400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:67086600-67096000	Weak transcription	Brain Hippocampus Middle	brain
19	chr11:67086600-67097800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr11:67086600-67099600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:67086600-67100600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:67086600-67103800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:67086600-67111200	Weak transcription	Primary B cells from cord blood	blood
24	chr11:67086600-67111200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:67086600-67118400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr11:67086800-67091200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:67086800-67092800	Weak transcription	Dnd41	blood
28	chr11:67086800-67099000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:67086800-67099000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:67086800-67100200	Weak transcription	Colon Smooth Muscle	Colon
31	chr11:67086800-67101200	Weak transcription	A549	lung
32	chr11:67086800-67118800	Weak transcription	Fetal Brain Male	brain
33	chr11:67087000-67092200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:67087000-67099000	Weak transcription	NHEK	skin
35	chr11:67087000-67100400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:67087000-67101200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:67087000-67111800	Weak transcription	Gastric	stomach
38	chr11:67087000-67112800	Weak transcription	Hela-S3	cervix
39	chr11:67087000-67113400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr11:67087800-67113800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:67087800-67119000	Weak transcription	Fetal Brain Female	brain
42	chr11:67088000-67103000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:67088200-67101400	Weak transcription	Ovary	ovary
44	chr11:67088400-67091200	Strong transcription	Fetal Stomach	stomach
45	chr11:67088400-67100800	Weak transcription	Right Ventricle	heart
46	chr11:67088600-67091000	Genic enhancers	Fetal Intestine Small	intestine
47	chr11:67088800-67090800	Genic enhancers	Pancreas	Pancrea
48	chr11:67088800-67091600	Strong transcription	Stomach Smooth Muscle	stomach
49	chr11:67089000-67090800	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:67089200-67090600	Weak transcription	Duodenum Mucosa	Duodenum

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