Variant report

Variant	rs2298466
Chromosome Location	chr11:66011280-66011281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66004162..66006201-chr11:66009991..66012477,2	K562	blood:
2	chr11:66010596..66013412-chr11:66022956..66027010,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175115	Chromatin interaction
ENSG00000174996	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10750777	0.86[ASN][1000 genomes]
rs10750778	0.93[ASN][1000 genomes]
rs10750780	0.89[ASN][1000 genomes]
rs10750781	0.97[ASN][1000 genomes]
rs10791849	0.87[ASN][1000 genomes]
rs10791850	0.95[ASN][1000 genomes]
rs10791851	0.95[ASN][1000 genomes]
rs10791852	0.95[ASN][1000 genomes]
rs10791854	0.98[ASN][1000 genomes]
rs10791855	0.98[ASN][1000 genomes]
rs10791858	1.00[ASN][1000 genomes]
rs10791859	1.00[ASN][1000 genomes]
rs10791860	0.97[ASN][1000 genomes]
rs10791861	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10791862	0.96[ASN][1000 genomes]
rs10791863	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10896077	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10896080	0.87[ASN][1000 genomes]
rs10896081	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10896085	0.90[ASN][1000 genomes]
rs10896087	0.90[ASN][1000 genomes]
rs10896089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10896090	0.95[ASN][1000 genomes]
rs10896091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10896093	0.96[ASN][1000 genomes]
rs10896094	0.96[ASN][1000 genomes]
rs10896098	0.97[ASN][1000 genomes]
rs10896099	0.98[ASN][1000 genomes]
rs10896100	0.97[ASN][1000 genomes]
rs10896105	0.97[ASN][1000 genomes]
rs11227403	0.83[ASN][1000 genomes]
rs11227409	0.87[ASN][1000 genomes]
rs11227410	0.87[ASN][1000 genomes]
rs11227411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11227413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11227414	0.87[ASN][1000 genomes]
rs11227415	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11227420	0.95[ASN][1000 genomes]
rs11227433	1.00[ASN][1000 genomes]
rs11227439	0.95[ASN][1000 genomes]
rs11227447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11227448	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11227452	0.91[ASN][1000 genomes]
rs11607393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12797158	0.98[ASN][1000 genomes]
rs12797586	0.89[ASN][1000 genomes]
rs12800670	0.98[ASN][1000 genomes]
rs1862005	0.84[ASN][1000 genomes]
rs2017969	0.96[ASN][1000 genomes]
rs2155030	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2155031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2155198	1.00[ASN][1000 genomes]
rs2155201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2177053	0.98[ASN][1000 genomes]
rs2177054	0.95[ASN][1000 genomes]
rs2236651	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2236652	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2276036	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs2282568	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2293121	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2298468	1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2889313	0.98[ASN][1000 genomes]
rs3132851	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs3814738	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3825067	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3862386	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3953856	0.98[ASN][1000 genomes]
rs4013917	0.90[ASN][1000 genomes]
rs4393319	1.00[ASN][1000 genomes]
rs4483592	1.00[ASN][1000 genomes]
rs476551	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs512421	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs560393	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6591207	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6591208	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7120326	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7124165	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7925123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7926402	0.87[ASN][1000 genomes]
rs7929909	0.95[ASN][1000 genomes]
rs7931477	0.90[ASN][1000 genomes]
rs7931544	0.90[ASN][1000 genomes]
rs7935336	0.87[ASN][1000 genomes]
rs7941431	0.97[ASN][1000 genomes]
rs7943911	0.95[ASN][1000 genomes]
rs7945723	0.97[ASN][1000 genomes]
rs7946917	0.89[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs7951079	0.97[ASN][1000 genomes]
rs918299	0.90[ASN][1000 genomes]
rs9645684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9736673	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2298466	ROM1	cis	parietal	SCAN
rs2298466	AHNAK	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65977600-66018600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:65984600-66024200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:65985800-66017800	Weak transcription	Fetal Heart	heart
4	chr11:65989600-66024200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:65990200-66019800	Strong transcription	Primary T cells from cord blood	blood
6	chr11:65990600-66015800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:65990600-66018400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:65990800-66018600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr11:65991000-66015400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:65991200-66012400	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr11:65991200-66018600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:65991200-66018600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:65991600-66012800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:65991600-66018400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:65991600-66018400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:65991800-66018400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr11:65993800-66018400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr11:65994400-66015200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:65994400-66018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:65994600-66013200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr11:65994600-66013800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:65994600-66018600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:65995000-66018000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:65995000-66018800	Strong transcription	Fetal Intestine Small	intestine
25	chr11:65995200-66015600	Strong transcription	Lung	lung
26	chr11:65995600-66012000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:65996000-66024400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:65996600-66011800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr11:65997400-66012600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:65997400-66013800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:65997400-66018600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:65997600-66012600	Strong transcription	Brain Anterior Caudate	brain
33	chr11:65997600-66012800	Strong transcription	Placenta	Placenta
34	chr11:65997600-66013600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:65997600-66013800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:65997600-66015400	Strong transcription	Brain Germinal Matrix	brain
37	chr11:65997600-66018400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:65997800-66012600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:65997800-66012800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:65997800-66012800	Strong transcription	Fetal Intestine Large	intestine
41	chr11:65997800-66012800	Strong transcription	Left Ventricle	heart
42	chr11:65997800-66012800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr11:65998000-66013800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:65998000-66018600	Strong transcription	Fetal Brain Female	brain
45	chr11:65999800-66013800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:65999800-66024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:66000800-66024200	Weak transcription	HMEC	breast
48	chr11:66001600-66024200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr11:66002000-66021000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:66003400-66017400	Weak transcription	Hela-S3	cervix

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