Variant report

Variant	rs7944560
Chromosome Location	chr11:8817276-8817277
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8715976..8718057-chr11:8817200..8820115,2	K562	blood:
2	chr11:8708277..8712745-chr11:8814108..8817920,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10769947	0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10769948	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10769955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769957	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769958	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10840147	0.81[CEU][hapmap]
rs11042055	0.92[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs11042059	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042060	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042067	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042078	0.83[GIH][hapmap]
rs12224436	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421789	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2316865	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742545	0.81[CEU][hapmap]
rs3763918	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3794153	0.92[CEU][hapmap]
rs4579928	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4929911	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929912	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929914	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4929916	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6484484	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484496	0.87[EUR][1000 genomes]
rs7107867	0.91[EUR][1000 genomes]
rs7129667	0.91[EUR][1000 genomes]
rs905290	0.92[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7944560	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs7944560	C11orf17	cis	multi-tissue	Pritchard
rs7944560	OR52A1	cis	parietal	SCAN
rs7944560	NRIP3	cis	parietal	SCAN
rs7944560	OR52E8	cis	cerebellum	SCAN
rs7944560	ST5	cis	parietal	SCAN
rs7944560	STK33	cis	cerebellum	SCAN
rs7944560	RRP8	cis	parietal	SCAN
rs7944560	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:8800800-8822400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:8800800-8825800	Weak transcription	Brain Angular Gyrus	brain
4	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:8801600-8820000	Weak transcription	HSMMtube	muscle
6	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
7	chr11:8802200-8819200	Weak transcription	NH-A	brain
8	chr11:8803000-8820600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:8808600-8819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
11	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
13	chr11:8810600-8820600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:8811800-8827000	Weak transcription	HMEC	breast
15	chr11:8811800-8828600	Weak transcription	Hela-S3	cervix
16	chr11:8811800-8828800	Weak transcription	Aorta	Aorta
17	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:8812400-8820600	Weak transcription	Right Ventricle	heart
20	chr11:8813800-8817600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr11:8814200-8828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:8814600-8817400	Weak transcription	NHEK	skin
23	chr11:8814800-8825400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr11:8815000-8827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:8815200-8818200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr11:8815200-8818800	Weak transcription	Adipose Nuclei	Adipose
27	chr11:8815200-8826800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:8815400-8818000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr11:8815400-8818600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr11:8815400-8819200	Weak transcription	Fetal Lung	lung
31	chr11:8815400-8820600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:8815400-8822000	Weak transcription	HUVEC	blood vessel
33	chr11:8815600-8822600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:8815600-8825200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:8815800-8817800	Strong transcription	Placenta	Placenta
36	chr11:8815800-8818200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:8815800-8827800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:8816000-8817800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:8816000-8822000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:8816200-8817600	Strong transcription	NHLF	lung
41	chr11:8816400-8818000	Enhancers	Stomach Mucosa	stomach
42	chr11:8816400-8818600	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr11:8816400-8819200	Weak transcription	Pancreas	Pancrea
44	chr11:8816400-8819400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr11:8816400-8819400	Weak transcription	HSMM	muscle
46	chr11:8816400-8822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:8816400-8822400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr11:8816400-8825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:8816400-8831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr11:8816600-8817600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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