Variant report

Variant	rs2434978
Chromosome Location	chr11:93488199-93488200
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	chr11:93471347..93475237-chr11:93486063..93491649,6	K562	blood:

Variant related genes	Relation type
ENSG00000182919	Chromatin interaction
ENSG00000166012	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10741476	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10765633	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10765634	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11020505	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11020506	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11020507	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12803773	0.88[AFR][1000 genomes]
rs1284102	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1284108	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1284141	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1783938	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2510603	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3132750	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3132751	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs595650	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs602242	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs602665	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs606286	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs606462	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs606749	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs607615	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs611762	0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs616876	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs618801	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs621355	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs624856	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs628661	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs630811	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs631177	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs631705	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs640379	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs640382	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs644535	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6483265	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs653939	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs659877	0.95[ASN][1000 genomes]
rs665507	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs666136	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs670871	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7943266	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7943525	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7950574	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2434978	C11orf54	Cis_1M	lymphoblastoid	RTeQTL
rs2434978	C11orf54	cis	Adipose Subcutaneous	GTEx
rs2434978	C11orf54	cis	Esophagus Mucosa	GTEx
rs2434978	C11orf54	cis	Stomach	GTEx
rs2434978	C11orf54	cis	Thyroid	GTEx
rs2434978	C11orf54	cis	lung	GTEx
rs2434978	C11orf54	cis	Heart Left Ventricle	GTEx
rs2434978	C11orf54	cis	Esophagus Muscularis	GTEx
rs2434978	C11orf54	cis	Nerve Tibial	GTEx
rs2434978	C11orf54	cis	Artery Aorta	GTEx
rs2434978	C11orf54	cis	Muscle Skeletal	GTEx
rs2434978	C11orf54	cis	multi-tissue	Pritchard
rs2434978	C11orf54	cis	Skin Sun Exposed Lower leg	GTEx
rs2434978	C11orf54	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93475200-93497000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:93475400-93490800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:93475400-93490800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:93475600-93490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:93475600-93497000	Weak transcription	NHDF-Ad	bronchial
6	chr11:93475800-93488400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:93475800-93488400	Weak transcription	Aorta	Aorta
8	chr11:93476000-93488400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:93476000-93488400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:93476000-93488400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:93476000-93488400	Weak transcription	HSMMtube	muscle
12	chr11:93476000-93490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:93476000-93491400	Weak transcription	Osteobl	bone
14	chr11:93476000-93495600	Weak transcription	HUVEC	blood vessel
15	chr11:93476000-93497000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:93476000-93497200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:93476000-93498800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:93476200-93499800	Weak transcription	NH-A	brain
19	chr11:93476600-93488400	Weak transcription	Colonic Mucosa	Colon
20	chr11:93477000-93488400	Weak transcription	Esophagus	oesophagus
21	chr11:93477000-93491200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:93477200-93488400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr11:93477200-93488400	Weak transcription	Spleen	Spleen
24	chr11:93477200-93490800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:93477200-93491400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:93477200-93491400	Weak transcription	NHLF	lung
27	chr11:93478200-93498800	Weak transcription	Fetal Heart	heart
28	chr11:93478400-93488400	Weak transcription	Right Ventricle	heart
29	chr11:93478400-93490600	Weak transcription	Psoas Muscle	Psoas
30	chr11:93478600-93488200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:93478600-93488400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr11:93478600-93488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:93478600-93488400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:93478600-93488400	Weak transcription	Fetal Brain Female	brain
35	chr11:93478600-93488400	Weak transcription	Left Ventricle	heart
36	chr11:93478600-93488400	Weak transcription	Ovary	ovary
37	chr11:93478600-93488400	Weak transcription	Pancreas	Pancrea
38	chr11:93478600-93488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:93478600-93488600	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:93478600-93489600	Weak transcription	Brain Substantia Nigra	brain
41	chr11:93478600-93489800	Weak transcription	K562	blood
42	chr11:93478600-93490400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:93478600-93490600	Weak transcription	Gastric	stomach
44	chr11:93478600-93498200	Weak transcription	Stomach Mucosa	stomach
45	chr11:93478800-93488400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:93478800-93488400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:93478800-93488400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:93478800-93488400	Weak transcription	Brain Germinal Matrix	brain
49	chr11:93478800-93508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:93479000-93490000	Weak transcription	Small Intestine	intestine

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