Variant report

Variant	rs1404976
Chromosome Location	chr11:73433135-73433136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10751229	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10793066	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10898930	0.80[AMR][1000 genomes]
rs10898935	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898936	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11235861	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11235862	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11235876	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11235883	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11235884	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11602887	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12361691	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12420357	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12788229	0.83[AMR][1000 genomes]
rs12788426	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1614987	0.82[EUR][1000 genomes]
rs1723843	0.82[EUR][1000 genomes]
rs1723848	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792166	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1792174	0.81[EUR][1000 genomes]
rs2140893	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2367187	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2367188	0.80[AMR][1000 genomes]
rs2462621	0.80[EUR][1000 genomes]
rs2511261	0.82[EUR][1000 genomes]
rs2512625	0.82[EUR][1000 genomes]
rs2512629	0.82[EUR][1000 genomes]
rs2886816	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4514449	0.80[EUR][1000 genomes]
rs7104603	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7119055	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7925514	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7933372	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938731	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs868667	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9705336	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv3409609	chr11:73433095-73433345	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1404976	MRPL48	cis	multi-tissue	Pritchard
rs1404976	MRPL48	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73382200-73436000	Weak transcription	Small Intestine	intestine
2	chr11:73382200-73441200	Weak transcription	Stomach Mucosa	stomach
3	chr11:73385000-73449800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:73389000-73445400	Weak transcription	Fetal Brain Male	brain
5	chr11:73389200-73440200	Weak transcription	Right Ventricle	heart
6	chr11:73391000-73433600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr11:73396000-73448000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:73400400-73449400	Weak transcription	Psoas Muscle	Psoas
9	chr11:73409600-73447800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:73410000-73434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr11:73411000-73447600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:73411000-73460000	Weak transcription	Colonic Mucosa	Colon
13	chr11:73413400-73440400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:73413400-73470800	Weak transcription	Esophagus	oesophagus
15	chr11:73413600-73447600	Weak transcription	Left Ventricle	heart
16	chr11:73415000-73436400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:73415000-73470200	Weak transcription	Aorta	Aorta
18	chr11:73417000-73440400	Weak transcription	Colon Smooth Muscle	Colon
19	chr11:73417200-73469600	Weak transcription	Fetal Kidney	kidney
20	chr11:73418200-73443400	Weak transcription	Brain Germinal Matrix	brain
21	chr11:73418400-73463200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr11:73422400-73443400	Weak transcription	Spleen	Spleen
23	chr11:73422400-73454000	Weak transcription	Gastric	stomach
24	chr11:73422800-73436000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:73422800-73448000	Weak transcription	Fetal Brain Female	brain
26	chr11:73426800-73435800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:73427600-73445600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:73427800-73433800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr11:73428000-73436200	Weak transcription	A549	lung
30	chr11:73428000-73445600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:73428400-73469800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:73428600-73440400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:73429000-73445400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:73429200-73439000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:73429600-73440800	Weak transcription	Brain Anterior Caudate	brain
36	chr11:73429800-73435800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:73429800-73436000	Weak transcription	K562	blood
38	chr11:73429800-73440800	Weak transcription	Brain Angular Gyrus	brain
39	chr11:73429800-73444800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr11:73429800-73446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:73430000-73434000	Weak transcription	Thymus	Thymus
42	chr11:73430000-73436000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:73430000-73440600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:73430000-73443600	Weak transcription	Ovary	ovary
45	chr11:73430000-73445800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:73430000-73446200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:73430000-73450400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr11:73430000-73451600	Weak transcription	HSMMtube	muscle
49	chr11:73430000-73460800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr11:73430200-73442200	Weak transcription	Pancreas	Pancrea

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