Variant report

Variant	rs4945229
Chromosome Location	chr11:77700197-77700198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77696988..77700525-chr11:77704022..77706318,4	K562	blood:
2	chr11:77699025..77702631-chr11:77704128..77707034,4	K562	blood:

Variant related genes	Relation type
ENSG00000149262	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1124590	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419883	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12420528	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575197	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12575337	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12577951	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17135969	0.83[EUR][1000 genomes]
rs1968666	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740681	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758664	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4944186	0.88[AMR][1000 genomes]
rs4945230	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57491077	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58992562	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59363412	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60124679	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60143695	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60355295	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60509203	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61201377	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61226220	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61487443	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67194469	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7107903	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72939484	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941310	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941320	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941328	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941334	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941336	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941350	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72941354	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7935050	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7946876	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4945229	AAMDC	cis	Thyroid	GTEx
rs4945229	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs4945229	RP11-91P24.7	cis	Artery Tibial	GTEx
rs4945229	RP11-91P24.7	cis	Thyroid	GTEx
rs4945229	RP11-91P24.6	cis	Artery Tibial	GTEx
rs4945229	AAMDC	cis	Artery Tibial	GTEx
rs4945229	RP11-91P24.6	cis	Thyroid	GTEx
rs4945229	RSF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
2	chr11:77649200-77701200	Weak transcription	NH-A	brain
3	chr11:77661400-77704400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:77664200-77704000	Weak transcription	NHEK	skin
5	chr11:77665800-77704200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:77666000-77704400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:77667600-77704200	Weak transcription	NHLF	lung
8	chr11:77668400-77701200	Weak transcription	Aorta	Aorta
9	chr11:77671200-77704200	Weak transcription	NHDF-Ad	bronchial
10	chr11:77672000-77701200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:77672000-77703800	Weak transcription	Fetal Brain Male	brain
12	chr11:77679000-77704200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr11:77680800-77700200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:77681000-77704200	Weak transcription	HSMMtube	muscle
15	chr11:77682000-77700200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:77682800-77700800	Weak transcription	Right Ventricle	heart
17	chr11:77684200-77702400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr11:77688200-77704800	Weak transcription	Stomach Mucosa	stomach
19	chr11:77688400-77702200	Strong transcription	Dnd41	blood
20	chr11:77688600-77702800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:77688800-77702400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr11:77688800-77702400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr11:77688800-77703400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:77688800-77703400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:77688800-77703800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:77689000-77702600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:77689000-77704800	Weak transcription	Fetal Heart	heart
28	chr11:77689200-77703000	Strong transcription	Primary T cells from cord blood	blood
29	chr11:77689200-77704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:77689400-77701400	Strong transcription	Primary B cells from peripheral blood	blood
31	chr11:77689600-77703000	Strong transcription	Fetal Thymus	thymus
32	chr11:77690400-77704200	Weak transcription	HMEC	breast
33	chr11:77690600-77700600	Weak transcription	Pancreas	Pancrea
34	chr11:77690600-77700800	Weak transcription	Esophagus	oesophagus
35	chr11:77690600-77700800	Weak transcription	Spleen	Spleen
36	chr11:77690600-77703800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:77690600-77704000	Weak transcription	Brain Anterior Caudate	brain
38	chr11:77690600-77704000	Weak transcription	Brain Substantia Nigra	brain
39	chr11:77690600-77704200	Weak transcription	Gastric	stomach
40	chr11:77690600-77704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:77690600-77704400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:77690800-77701000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:77690800-77704200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:77690800-77704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr11:77690800-77704200	Weak transcription	Small Intestine	intestine
46	chr11:77691400-77704000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:77691400-77704800	Weak transcription	Colonic Mucosa	Colon
48	chr11:77691800-77700400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:77691800-77700600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr11:77691800-77701800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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