Variant report

Variant	rs4561376
Chromosome Location	chr14:25411786-25411787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10483291	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs11159000	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs11159001	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs11847012	0.81[GIH][hapmap]
rs12586327	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs12586425	1.00[CEU][hapmap]
rs12880456	0.84[GIH][hapmap]
rs12885474	0.84[GIH][hapmap]
rs12887754	0.84[GIH][hapmap]
rs12896576	0.84[GIH][hapmap]
rs17185397	0.84[GIH][hapmap]
rs17185425	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs17257556	0.88[GIH][hapmap]
rs1951800	0.85[CEU][hapmap]
rs2038699	0.85[ASN][1000 genomes]
rs2332459	0.85[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs2877686	0.85[CEU][hapmap]
rs55687412	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59153576	0.83[ASN][1000 genomes]
rs7141066	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7155229	1.00[CEU][hapmap]
rs74040739	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74040740	0.81[AFR][1000 genomes]
rs8003472	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs912306	0.85[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs912307	0.85[CEU][hapmap]
rs9671261	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901508	chr14:25365505-25451903	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1041051	chr14:25388230-25480511	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1047792	chr14:25388933-25503799	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4561376	OR4K17	cis	cerebellum	SCAN
rs4561376	IDH2	trans	cerebellum	SCAN
rs4561376	RIPK3	cis	brain	BrainEAC

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25396600-25415800	Weak transcription	Fetal Brain Male	brain
2	chr14:25399400-25413800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr14:25399800-25413400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr14:25399800-25413600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:25403800-25411800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr14:25404600-25411800	Weak transcription	Brain Angular Gyrus	brain
7	chr14:25405200-25411800	Weak transcription	Brain Hippocampus Middle	brain
8	chr14:25405200-25411800	Weak transcription	Colon Smooth Muscle	Colon
9	chr14:25405400-25411800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr14:25405600-25412400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr14:25406400-25412200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr14:25407400-25413200	Weak transcription	Brain Anterior Caudate	brain
13	chr14:25408200-25411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr14:25408400-25412200	Weak transcription	HSMM	muscle
15	chr14:25408400-25412400	Enhancers	Fetal Heart	heart
16	chr14:25408600-25411800	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr14:25408600-25412000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr14:25409000-25412400	Enhancers	GM12878-XiMat	blood
19	chr14:25409800-25411800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr14:25409800-25412600	Enhancers	Pancreas	Pancrea
21	chr14:25409800-25412800	Enhancers	Left Ventricle	heart
22	chr14:25410000-25412600	Enhancers	Right Atrium	heart
23	chr14:25410000-25414200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:25410400-25411800	Strong transcription	Fetal Muscle Leg	muscle
25	chr14:25410400-25412000	Enhancers	H9 Cell Line	embryonic stem cell
26	chr14:25410400-25412200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr14:25410400-25412400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr14:25410400-25412600	Enhancers	Fetal Intestine Large	intestine
29	chr14:25410400-25412800	Enhancers	Fetal Thymus	thymus
30	chr14:25410400-25413400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr14:25410400-25413600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr14:25410600-25412600	Enhancers	Fetal Intestine Small	intestine
33	chr14:25410600-25412600	Enhancers	Fetal Lung	lung
34	chr14:25410600-25413000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr14:25410600-25414200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr14:25410800-25412000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr14:25410800-25412000	Genic enhancers	HepG2	liver
38	chr14:25410800-25412800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr14:25410800-25414200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr14:25411000-25412200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr14:25411000-25412600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr14:25411200-25412000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr14:25411200-25412200	Weak transcription	Small Intestine	intestine
44	chr14:25411200-25412400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr14:25411200-25412400	Weak transcription	Gastric	stomach
46	chr14:25411200-25412600	Enhancers	Duodenum Mucosa	Duodenum
47	chr14:25411400-25412200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr14:25411600-25411800	Enhancers	Lung	lung
49	chr14:25411600-25412000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr14:25411600-25412400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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