Variant report

Variant	rs3862138
Chromosome Location	chr15:43815999-43816000
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	chr15:43809318..43812744-chr15:43815463..43818743,6	K562	blood:
2	chr15:43806460..43809069-chr15:43815208..43818201,3	K562	blood:

Variant related genes	Relation type
ENSG00000166963	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10518812	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap]
rs11554564	1.00[CHB][hapmap]
rs12899865	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12900259	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12905220	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12906017	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12906481	0.90[EUR][1000 genomes]
rs12907870	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12908460	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12910639	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12911740	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12912744	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap]
rs12913977	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12914122	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16957680	0.95[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs16957715	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16957730	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17727853	0.80[AMR][1000 genomes]
rs17780417	0.95[CEU][hapmap]
rs17780920	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap]
rs17795279	0.86[TSI][hapmap]
rs2230451	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28903076	1.00[CHB][hapmap]
rs34002293	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34181131	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34388946	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633582	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34661349	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34697113	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34860428	0.84[EUR][1000 genomes]
rs34921640	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35158584	0.81[EUR][1000 genomes]
rs35903301	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35958032	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36078097	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs514438	0.95[CEU][hapmap];0.81[MEX][hapmap]
rs55801120	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56246169	0.80[AMR][1000 genomes]
rs57728767	0.82[EUR][1000 genomes]
rs57938858	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60018990	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60367691	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62020574	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62020575	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62020612	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62020616	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62021180	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs66629206	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7048	0.81[GIH][hapmap];0.87[YRI][hapmap]
rs71476435	0.90[EUR][1000 genomes]
rs7173383	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7177146	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7180812	0.95[CEU][hapmap];0.96[GIH][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes]
rs7181634	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap]
rs7181783	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7182292	0.90[EUR][1000 genomes]
rs72709850	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72709879	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8027748	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8030536	0.86[TSI][hapmap]
rs8038068	0.86[TSI][hapmap];0.80[AMR][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	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv437799	chr15:43784000-43989518	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv515877	chr15:43802024-43818052	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv518707	chr15:43802024-43826557	Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv832988	chr15:43804641-43976862	Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3862138	ZSCAN29	cis	lymphoblastoid	seeQTL
rs3862138	DUOXA1	cis	parietal	SCAN
rs3862138	LCMT2	cis	Esophagus Mucosa	GTEx
rs3862138	ZFP106	cis	cerebellum	SCAN
rs3862138	ADAL	cis	cerebellum	SCAN
rs3862138	TUBGCP4	cis	Artery Tibial	GTEx
rs3862138	TGM7	cis	Esophagus Mucosa	GTEx
rs3862138	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43810400-43826200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:43810600-43826400	Weak transcription	Spleen	Spleen
3	chr15:43810800-43817600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:43810800-43824000	Weak transcription	Fetal Kidney	kidney
5	chr15:43810800-43826000	Weak transcription	Esophagus	oesophagus
6	chr15:43811000-43818600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:43811000-43828600	Weak transcription	Pancreas	Pancrea
8	chr15:43811200-43820600	Weak transcription	Colonic Mucosa	Colon
9	chr15:43811200-43823600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:43811200-43826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:43811400-43829200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:43812000-43823200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr15:43812000-43844400	Weak transcription	Fetal Brain Male	brain
14	chr15:43812200-43818000	Strong transcription	Fetal Intestine Large	intestine
15	chr15:43812200-43819000	Strong transcription	Osteobl	bone
16	chr15:43812200-43823200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:43812200-43823800	Strong transcription	NHLF	lung
18	chr15:43812400-43817800	ZNF genes & repeats	Aorta	Aorta
19	chr15:43812400-43818200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:43812400-43819000	ZNF genes & repeats	Fetal Stomach	stomach
21	chr15:43812400-43821400	Strong transcription	HSMMtube	muscle
22	chr15:43812400-43823200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:43812600-43816400	Genic enhancers	Brain Angular Gyrus	brain
24	chr15:43812600-43816400	Genic enhancers	Brain Anterior Caudate	brain
25	chr15:43812600-43816400	Strong transcription	Thymus	Thymus
26	chr15:43812600-43817600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:43812600-43817800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:43812600-43818200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:43812600-43818200	Strong transcription	Left Ventricle	heart
30	chr15:43812600-43818800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:43812600-43819600	Strong transcription	HSMM	muscle
32	chr15:43812600-43819600	Strong transcription	NH-A	brain
33	chr15:43812600-43820000	Genic enhancers	Brain Hippocampus Middle	brain
34	chr15:43812600-43820400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:43812600-43823200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:43812600-43823200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:43812800-43816000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:43812800-43816200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr15:43812800-43816600	Strong transcription	Primary T cells from cord blood	blood
40	chr15:43812800-43817600	Strong transcription	Fetal Lung	lung
41	chr15:43812800-43818000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:43812800-43818000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr15:43812800-43818200	Strong transcription	Colon Smooth Muscle	Colon
44	chr15:43812800-43818800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:43812800-43819800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:43812800-43820200	Strong transcription	NHDF-Ad	bronchial
47	chr15:43812800-43822400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:43812800-43823200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:43812800-43823800	Strong transcription	Brain Germinal Matrix	brain
50	chr15:43812800-43824200	Strong transcription	Fetal Brain Female	brain

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