Variant report

Variant	rs12794444
Chromosome Location	chr11:8826559-8826560
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8820429..8822256-chr11:8823665..8826630,2	K562	blood:
2	chr11:8776493..8778441-chr11:8825146..8827348,2	MCF-7	breast:
3	chr11:8825764..8827558-chr11:8831066..8834335,3	K562	blood:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10769955	0.82[AMR][1000 genomes]
rs10769957	0.81[AMR][1000 genomes]
rs10769967	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840130	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840134	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11042069	0.81[AMR][1000 genomes]
rs11042078	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042079	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042082	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042088	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603841	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1529641	0.90[EUR][1000 genomes]
rs2316865	0.81[AMR][1000 genomes]
rs2568043	0.90[EUR][1000 genomes]
rs2568090	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2653606	0.91[EUR][1000 genomes]
rs2653607	0.90[EUR][1000 genomes]
rs4554887	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910062	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4929916	0.81[AMR][1000 genomes]
rs61876187	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7119939	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7123429	0.82[EUR][1000 genomes]
rs7937298	0.82[EUR][1000 genomes]
rs7943377	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs978636	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12794444	TMEM9B-AS1	cis	lung	GTEx
rs12794444	AKIP1	cis	Thyroid	GTEx
rs12794444	TMEM9B-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 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	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
4	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
5	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
7	chr11:8811800-8827000	Weak transcription	HMEC	breast
8	chr11:8811800-8828600	Weak transcription	Hela-S3	cervix
9	chr11:8811800-8828800	Weak transcription	Aorta	Aorta
10	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:8814200-8828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr11:8815000-8827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:8815200-8826800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:8815800-8827800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:8816400-8831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:8816600-8826600	Weak transcription	Brain Anterior Caudate	brain
18	chr11:8816600-8827400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr11:8816600-8828400	Weak transcription	NHDF-Ad	bronchial
20	chr11:8816600-8828800	Weak transcription	Brain Substantia Nigra	brain
21	chr11:8816600-8830000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr11:8816600-8830600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:8816800-8828600	Weak transcription	Small Intestine	intestine
24	chr11:8817000-8828600	Weak transcription	Fetal Intestine Large	intestine
25	chr11:8817200-8828600	Weak transcription	Fetal Intestine Small	intestine
26	chr11:8817400-8828200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:8819200-8826600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:8819800-8828600	Weak transcription	Osteobl	bone
29	chr11:8819800-8829800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr11:8820000-8828200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:8821200-8826600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:8821400-8827600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:8821600-8830200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr11:8822200-8826600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:8822200-8827200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:8822200-8827400	Weak transcription	Psoas Muscle	Psoas
37	chr11:8822200-8828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:8822400-8826600	Weak transcription	HSMM	muscle
39	chr11:8822400-8828400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr11:8822600-8827400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:8822600-8828200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:8822800-8826600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:8822800-8826800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr11:8822800-8827200	Weak transcription	Fetal Heart	heart
45	chr11:8823000-8826600	Weak transcription	Colonic Mucosa	Colon
46	chr11:8823000-8826600	Enhancers	Colon Smooth Muscle	Colon
47	chr11:8823000-8826600	Weak transcription	Fetal Lung	lung
48	chr11:8823000-8827400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:8823000-8827600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:8823200-8827600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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