Variant report

Variant	rs11729215
Chromosome Location	chr4:78725120-78725121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78724686..78728038-chr4:78739798..78742986,3	K562	blood:

Variant related genes	Relation type
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10033527	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10033613	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11097938	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11728886	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645742	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13101418	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs13101987	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13103035	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13103523	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13104947	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13106067	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13120272	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16996915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2134050	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28404443	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28855210	0.85[ASN][1000 genomes]
rs34830788	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35735677	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4453957	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4571357	0.86[ASN][1000 genomes]
rs4577601	0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs4859509	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4859511	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4859875	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4859877	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4859879	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859888	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4859889	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs6533282	0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6533291	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6533344	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[MKK][hapmap]
rs6814912	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs6848029	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6854895	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7670157	0.86[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7675009	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7676660	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7698627	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.94[ASN][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	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11729215	MRPL1	cis	parietal	SCAN
rs11729215	MRPL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78716400-78733400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:78718200-78728200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:78718800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:78720600-78732000	Weak transcription	Aorta	Aorta
5	chr4:78720800-78735600	Weak transcription	HepG2	liver
6	chr4:78721000-78732400	Weak transcription	Fetal Intestine Small	intestine
7	chr4:78722200-78738600	Weak transcription	HSMM	muscle
8	chr4:78722400-78727000	Weak transcription	Stomach Mucosa	stomach
9	chr4:78722400-78727800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr4:78722400-78734800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:78722600-78725400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr4:78722600-78725600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr4:78722600-78725600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:78722600-78725600	Weak transcription	Osteobl	bone
15	chr4:78722600-78728600	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:78722600-78729000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr4:78722600-78732000	Weak transcription	Thymus	Thymus
18	chr4:78722600-78735800	Weak transcription	A549	lung
19	chr4:78722600-78737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:78722600-78737800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:78722600-78738600	Weak transcription	NHEK	skin
22	chr4:78722600-78739000	Weak transcription	Ovary	ovary
23	chr4:78722600-78739200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:78722800-78732000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:78722800-78736800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:78722800-78738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:78723000-78732000	Weak transcription	Right Atrium	heart
28	chr4:78723000-78732400	Weak transcription	Fetal Thymus	thymus
29	chr4:78723000-78732600	Enhancers	Primary T cells from cord blood	blood
30	chr4:78723000-78734800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:78723000-78738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:78723200-78725400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:78723200-78726600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:78723200-78726800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr4:78723200-78726800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr4:78723200-78727000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:78723200-78728600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:78723200-78738600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:78723600-78725800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:78723800-78725400	Weak transcription	Brain Anterior Caudate	brain
41	chr4:78724000-78726000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr4:78724000-78726000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:78724000-78726000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:78724000-78726400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:78724000-78732000	Weak transcription	Dnd41	blood
46	chr4:78724000-78735000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:78724000-78736000	Weak transcription	HUVEC	blood vessel
48	chr4:78724000-78736800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:78724200-78726000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:78724200-78726400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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