Variant report

Variant	rs11828339
Chromosome Location	chr11:47404314-47404315
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	chr11:47391440..47404809-chr11:47427075..47436409,23	K562	blood:

Variant related genes	Relation type
ENSG00000165915	Chromatin interaction
ENSG00000255197	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1044269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1051006	0.81[CEU][hapmap]
rs10742805	0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10742806	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10769253	0.81[CEU][hapmap]
rs10769255	0.91[CEU][hapmap]
rs10769267	0.80[ASN][1000 genomes]
rs10838689	0.81[CEU][hapmap]
rs11039194	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11819955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11820650	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11821273	0.82[ASN][1000 genomes]
rs11821860	0.80[ASN][1000 genomes]
rs11821917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11822402	0.80[ASN][1000 genomes]
rs11823490	0.80[EUR][1000 genomes]
rs11824864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11824971	0.81[EUR][1000 genomes]
rs11827106	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12419342	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs17198158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17790804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242511	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290148	0.81[CEU][hapmap]
rs3729802	0.85[CEU][hapmap]
rs3740684	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs3740685	0.81[ASN][1000 genomes]
rs3781628	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3824867	0.88[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3847503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4237544	0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4282946	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4384349	0.83[ASN][1000 genomes]
rs4752783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4752829	0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4752836	0.81[ASN][1000 genomes]
rs4752837	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4752839	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4752842	0.82[MEX][hapmap]
rs4752843	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs4752977	0.81[CEU][hapmap]
rs4752983	0.81[CEU][hapmap]
rs4752992	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56756748	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59631865	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60380053	0.82[ASN][1000 genomes]
rs60882887	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60929305	0.81[EUR][1000 genomes]
rs61000762	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7101772	0.83[ASN][1000 genomes]
rs7104366	0.80[ASN][1000 genomes]
rs7105122	0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7105907	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7106142	0.82[ASN][1000 genomes]
rs7107853	0.81[ASN][1000 genomes]
rs7108143	0.80[ASN][1000 genomes]
rs7111873	0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7117277	0.82[ASN][1000 genomes]
rs7119556	0.80[ASN][1000 genomes]
rs7126210	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7130693	0.82[ASN][1000 genomes]
rs753812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs753992	0.81[CEU][hapmap]
rs7948705	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9666924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs9734013	0.82[ASN][1000 genomes]
rs9919526	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11828339	TTC17	cis	cerebellum	SCAN
rs11828339	SLC35C1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47395200-47410000	Weak transcription	Gastric	stomach
2	chr11:47399400-47421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:47399800-47405000	Weak transcription	Right Atrium	heart
4	chr11:47399800-47405800	Weak transcription	Brain Angular Gyrus	brain
5	chr11:47399800-47421200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:47400000-47410000	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:47400000-47415200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:47400000-47416000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:47400000-47416800	Weak transcription	Brain Anterior Caudate	brain
10	chr11:47400000-47421200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:47400600-47409800	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:47401200-47404400	Weak transcription	Primary B cells from cord blood	blood
13	chr11:47402600-47409400	Weak transcription	Esophagus	oesophagus
14	chr11:47403200-47405400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
15	chr11:47403400-47405000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:47403600-47405400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:47404000-47404400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:47404000-47404400	Bivalent Enhancer	Placenta	Placenta
19	chr11:47404000-47404600	Enhancers	HUVEC	blood vessel
20	chr11:47404000-47404800	Enhancers	Spleen	Spleen
21	chr11:47404000-47405200	Enhancers	Lung	lung
22	chr11:47404000-47405400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
23	chr11:47404000-47405800	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr11:47404200-47404400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:47404200-47404400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:47404200-47404800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr11:47404200-47405000	Enhancers	K562	blood
28	chr11:47404200-47405200	Enhancers	Fetal Muscle Trunk	muscle
29	chr11:47404200-47405400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr11:47404200-47405400	Enhancers	Adipose Nuclei	Adipose

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