Variant report

Variant	rs7177146
Chromosome Location	chr15:43798308-43798309
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr15:43797722-43798549	IMR90	lung:	n/a	n/a
2	MAFK	chr15:43797918-43798324	IMR90	lung:	n/a	chr15:43798077-43798087

No.	Distal block	Cell Line	Cell type
1	chr15:43791785..43793850-chr15:43798056..43800431,2	K562	blood:
2	15:43792489-43802874..15:44074989-44078735	K562	blood:
3	chr15:43797635..43799443-chr15:43800947..43803863,2	K562	blood:
4	chr15:43781846..43787403-chr15:43796763..43800745,6	K562	blood:
5	15:43792489-43802874..15:44001645-44015047	GM12878	blood:
6	chr15:43797925..43800191-chr15:43800913..43803440,3	K562	blood:

Variant related genes	Relation type
MAP1A	TF binding region
ENSG00000067369	Chromatin interaction
ENSG00000166763	Chromatin interaction
ENSG00000242866	Chromatin interaction
ENSG00000166963	Chromatin interaction
ENSG00000268488	Chromatin interaction
ENSG00000238494	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10518812	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12899865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12900259	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12905220	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12906017	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12906481	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12907870	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12908460	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12910639	0.82[EUR][1000 genomes]
rs12911569	0.85[AMR][1000 genomes]
rs12911740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912744	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap]
rs12913977	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12914122	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957680	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16957715	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16957730	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17723479	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs17780417	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17780920	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2230451	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34002293	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34178146	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34181131	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34212866	0.90[AFR][1000 genomes]
rs34388946	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34515241	0.80[AMR][1000 genomes]
rs34591748	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34633582	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34661349	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34697113	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34767197	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34860428	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34921640	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35158584	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35160541	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35278805	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35326382	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35903301	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35958032	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35992154	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36078097	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3862138	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]
rs514438	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs55748552	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55801120	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57728767	0.88[EUR][1000 genomes]
rs57938858	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60018990	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60367691	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62019432	0.83[AMR][1000 genomes]
rs62020574	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62020575	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62020612	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62020616	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62021176	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62021180	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66629206	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7048	0.90[ASW][hapmap];0.81[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap]
rs71476435	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7173383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7176923	0.95[CEU][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs7177892	0.83[AMR][1000 genomes]
rs7180812	0.90[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7181545	0.83[AMR][1000 genomes]
rs7181634	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7181783	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7182292	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7183708	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72707530	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72709850	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72709879	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8027748	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7177146	LCMT2	cis	Esophagus Mucosa	GTEx
rs7177146	DUOXA1	cis	parietal	SCAN
rs7177146	TUBGCP4	cis	cerebellum	SCAN
rs7177146	ZSCAN29	cis	multi-tissue	Pritchard
rs7177146	FLJ35867	cis	multi-tissue	Pritchard
rs7177146	ZFP106	cis	cerebellum	SCAN
rs7177146	ADAL	cis	cerebellum	SCAN
rs7177146	TGM7	cis	Esophagus Mucosa	GTEx
rs7177146	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs7177146	TUBGCP4	cis	Artery Tibial	GTEx
rs7177146	ZSCAN29	cis	lymphoblastoid	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43786000-43801800	Weak transcription	Primary T cells from cord blood	blood
2	chr15:43786200-43801200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:43786200-43801200	Weak transcription	Ovary	ovary
4	chr15:43786400-43801000	Weak transcription	Dnd41	blood
5	chr15:43789400-43801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:43794200-43802000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:43795400-43801800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:43796200-43800600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:43796600-43802000	Weak transcription	Aorta	Aorta
10	chr15:43796800-43802000	Weak transcription	Fetal Kidney	kidney
11	chr15:43797400-43799200	Enhancers	HSMM	muscle
12	chr15:43797400-43799200	Enhancers	HSMMtube	muscle
13	chr15:43797400-43799400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:43797600-43798800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:43797600-43798800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:43797600-43798800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:43797600-43798800	Enhancers	Fetal Stomach	stomach
18	chr15:43797600-43798800	Enhancers	Osteobl	bone
19	chr15:43797600-43799000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:43797600-43799000	Enhancers	NHDF-Ad	bronchial
21	chr15:43797600-43799200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr15:43797600-43799200	Enhancers	K562	blood
23	chr15:43797800-43798400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:43797800-43798400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:43797800-43798400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:43797800-43798800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:43797800-43799000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:43797800-43799000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:43797800-43799000	Enhancers	Fetal Lung	lung
30	chr15:43797800-43799200	Enhancers	Fetal Muscle Leg	muscle
31	chr15:43798000-43798400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:43798000-43798400	Enhancers	Fetal Thymus	thymus
33	chr15:43798000-43798400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr15:43798000-43798600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:43798000-43798800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr15:43798000-43799000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr15:43798200-43798600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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