Variant report

Variant	rs13377546
Chromosome Location	chr11:77699087-77699088
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: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11237326	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11237328	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237329	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237333	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11237335	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11237338	0.87[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237341	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11237347	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11501934	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603727	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11605955	0.86[EUR][1000 genomes]
rs11606909	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606971	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11607479	0.87[EUR][1000 genomes]
rs11607512	0.81[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12273552	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12279880	0.87[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12284929	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12289316	0.83[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12289587	0.82[ASN][1000 genomes]
rs12292039	0.88[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12293597	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12799701	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17752458	0.81[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825404	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823507	0.88[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305317	0.87[CEU][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4123593	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4123595	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55878159	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55962013	0.82[EUR][1000 genomes]
rs57055061	0.83[EUR][1000 genomes]
rs695046	0.91[YRI][hapmap]
rs7115801	0.87[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7119720	0.87[EUR][1000 genomes]
rs7131359	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs72939500	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941332	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72941339	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72941353	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947841	0.91[YRI][hapmap]
rs9630225	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13377546	INTS4	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	chr11:77689200-77700000	Strong transcription	Primary B cells from cord blood	blood
29	chr11:77689200-77703000	Strong transcription	Primary T cells from cord blood	blood
30	chr11:77689200-77704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:77689400-77701400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr11:77689600-77703000	Strong transcription	Fetal Thymus	thymus
33	chr11:77690400-77704200	Weak transcription	HMEC	breast
34	chr11:77690600-77700600	Weak transcription	Pancreas	Pancrea
35	chr11:77690600-77700800	Weak transcription	Esophagus	oesophagus
36	chr11:77690600-77700800	Weak transcription	Spleen	Spleen
37	chr11:77690600-77703800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr11:77690600-77704000	Weak transcription	Brain Anterior Caudate	brain
39	chr11:77690600-77704000	Weak transcription	Brain Substantia Nigra	brain
40	chr11:77690600-77704200	Weak transcription	Gastric	stomach
41	chr11:77690600-77704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:77690600-77704400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:77690800-77701000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr11:77690800-77704200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:77690800-77704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr11:77690800-77704200	Weak transcription	Small Intestine	intestine
47	chr11:77691000-77700000	Weak transcription	Fetal Brain Female	brain
48	chr11:77691400-77704000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:77691400-77704800	Weak transcription	Colonic Mucosa	Colon
50	chr11:77691800-77699400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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