Variant report

Variant	rs11097938
Chromosome Location	chr4:78735895-78735896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78734703..78743448-chr4:78779372..78785561,20	K562	blood:
2	chr4:78721732..78724295-chr4:78733166..78737485,4	K562	blood:
3	chr4:78727738..78737799-chr4:78737984..78742271,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10033527	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10033613	0.96[ASN][1000 genomes]
rs11728886	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11729215	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]
rs12645742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13101418	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs13101987	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs13103035	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13103523	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13104947	0.82[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs13106067	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs13119606	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13120272	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16996915	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2088992	0.89[JPT][hapmap]
rs2134050	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28404443	0.90[ASN][1000 genomes]
rs28855210	0.85[ASN][1000 genomes]
rs34830788	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35735677	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4453957	0.96[ASN][1000 genomes]
rs4571357	0.86[ASN][1000 genomes]
rs4577601	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4859509	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4859511	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4859875	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4859877	0.82[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859888	0.90[ASN][1000 genomes]
rs4859889	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6533282	0.85[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6533291	0.96[ASN][1000 genomes]
rs6533344	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap]
rs6814912	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs6848029	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6854895	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7670157	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7675009	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.96[ASN][1000 genomes]
rs7676660	0.89[ASN][1000 genomes]
rs7698627	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];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
rs11097938	MRPL1	cis	parietal	SCAN
rs11097938	MRPL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78718800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:78722200-78738600	Weak transcription	HSMM	muscle
3	chr4:78722600-78737800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:78722600-78737800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:78722600-78738600	Weak transcription	NHEK	skin
6	chr4:78722600-78739000	Weak transcription	Ovary	ovary
7	chr4:78722600-78739200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:78722800-78736800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:78722800-78738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:78723000-78738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:78723200-78738600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:78724000-78736000	Weak transcription	HUVEC	blood vessel
13	chr4:78724000-78736800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:78724400-78738600	Weak transcription	Colonic Mucosa	Colon
15	chr4:78724800-78738600	Weak transcription	Brain Substantia Nigra	brain
16	chr4:78725800-78736800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr4:78725800-78738600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr4:78727200-78737800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr4:78728600-78738600	Weak transcription	Psoas Muscle	Psoas
20	chr4:78728800-78736600	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:78728800-78738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr4:78729000-78736600	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:78730400-78738600	Weak transcription	K562	blood
24	chr4:78732200-78736200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:78732200-78736400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:78732200-78736400	Weak transcription	Brain Anterior Caudate	brain
27	chr4:78732200-78736600	Weak transcription	Aorta	Aorta
28	chr4:78732200-78738600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:78732400-78738600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:78732800-78738800	Weak transcription	Lung	lung
31	chr4:78733200-78736600	Weak transcription	Small Intestine	intestine
32	chr4:78733200-78738600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr4:78733400-78738000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:78733600-78736400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr4:78733600-78736400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:78733600-78738600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:78733800-78736600	Weak transcription	Fetal Thymus	thymus
38	chr4:78734000-78736600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr4:78734200-78736400	Enhancers	Dnd41	blood
40	chr4:78734200-78736600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:78734600-78736600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:78734600-78737200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr4:78734800-78737000	Enhancers	Fetal Intestine Large	intestine
44	chr4:78734800-78738600	Enhancers	Duodenum Mucosa	Duodenum
45	chr4:78735000-78738000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:78735200-78736000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr4:78735200-78736600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:78735200-78736600	Weak transcription	Adipose Nuclei	Adipose
49	chr4:78735200-78736600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:78735200-78737400	Enhancers	Duodenum Smooth Muscle	Duodenum

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