Variant report

Variant	rs12456084
Chromosome Location	chr18:39646221-39646222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10221315	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10468957	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10775471	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11082255	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11082257	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12326267	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12455038	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12455083	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12455780	0.81[EUR][1000 genomes]
rs12456573	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12456761	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12456934	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12457082	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12457086	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12457354	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12457525	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12964834	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12964931	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12966303	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13381503	0.82[EUR][1000 genomes]
rs1368025	0.80[EUR][1000 genomes]
rs1432138	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1557418	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1573497	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16975474	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1941526	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1941532	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1942151	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1942152	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1984366	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1984367	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2043220	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2156015	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34966612	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4121647	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4890221	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4890377	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4890378	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4890379	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs5004531	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510946	0.83[EUR][1000 genomes]
rs56147258	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56211042	0.83[AMR][1000 genomes]
rs569983	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57794431	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs581950	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs60861018	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61107251	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62082282	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62082880	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62082911	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs627099	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs639660	0.86[EUR][1000 genomes]
rs650586	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6507451	0.80[EUR][1000 genomes]
rs657164	0.94[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs667503	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66960332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237459	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7504589	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8093251	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304263	0.81[EUR][1000 genomes]
rs948873	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9635942	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9807114	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9807279	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9807400	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9948913	0.81[EUR][1000 genomes]
rs9989595	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription 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 target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1057988	chr18:39618253-39713904	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv1065792	chr18:39619676-39711798	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	nsv1057790	chr18:39621947-39705550	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	esv2762006	chr18:39621947-39713916	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1063952	chr18:39621947-39718600	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv1064973	chr18:39623604-39711798	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	nsv833631	chr18:39633503-39824091	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12456084	CELF4	cis	cerebellum	SCAN
rs12456084	PIK3C3	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
3	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
4	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
5	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
7	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
8	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
9	chr18:39601600-39668200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr18:39612200-39647400	Weak transcription	Aorta	Aorta
11	chr18:39612200-39666400	Weak transcription	Gastric	stomach
12	chr18:39612200-39669800	Weak transcription	Fetal Stomach	stomach
13	chr18:39612200-39670000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr18:39615000-39649600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr18:39615400-39663400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr18:39618000-39647400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr18:39619200-39656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:39619400-39647600	Weak transcription	Brain Germinal Matrix	brain
19	chr18:39619600-39647400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr18:39619800-39662200	Weak transcription	Right Ventricle	heart
21	chr18:39620800-39664200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr18:39621200-39657200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr18:39622200-39649400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr18:39628600-39666200	Weak transcription	A549	lung
25	chr18:39629000-39649600	Weak transcription	NHLF	lung
26	chr18:39630600-39647400	Weak transcription	Colon Smooth Muscle	Colon
27	chr18:39630600-39658600	Weak transcription	Hela-S3	cervix
28	chr18:39630800-39650200	Weak transcription	Fetal Kidney	kidney
29	chr18:39631000-39647400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr18:39631200-39647000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr18:39631200-39647200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr18:39631200-39647200	Weak transcription	HepG2	liver
33	chr18:39631200-39647400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr18:39631200-39647400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr18:39631200-39650200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr18:39631200-39659800	Weak transcription	Fetal Brain Male	brain
37	chr18:39631400-39647200	Weak transcription	HMEC	breast
38	chr18:39631400-39650000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr18:39633200-39646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr18:39633200-39652400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr18:39633600-39647200	Weak transcription	Brain Angular Gyrus	brain
42	chr18:39633600-39647200	Weak transcription	Brain Substantia Nigra	brain
43	chr18:39634000-39647400	Weak transcription	Fetal Intestine Large	intestine
44	chr18:39634000-39647800	Weak transcription	Fetal Intestine Small	intestine
45	chr18:39634800-39674600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr18:39635000-39648000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr18:39638000-39647200	Weak transcription	NH-A	brain
48	chr18:39638600-39647200	Weak transcription	Fetal Muscle Leg	muscle
49	chr18:39638800-39647000	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr18:39639200-39647200	Weak transcription	Primary hematopoietic stem cells	blood

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