Variant report

Variant	rs35326382
Chromosome Location	chr15:43630884-43630885
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43625690..43629602-chr15:43629922..43634519,5	K562	blood:
2	chr15:43621044..43624825-chr15:43626235..43637209,16	K562	blood:
3	chr15:43621240..43623334-chr15:43630351..43632942,2	MCF-7	breast:
4	chr15:43620805..43624764-chr15:43626235..43634573,14	K562	blood:
5	chr15:43625690..43627311-chr15:43629922..43632321,2	K562	blood:

Variant related genes	Relation type
ENSG00000168806	Chromatin interaction
ENSG00000168803	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10518812	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899865	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12900259	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12905220	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12906017	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12906481	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12907870	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12908460	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911569	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12911740	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12913977	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12914122	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16957680	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957715	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957730	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17723479	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17780417	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17780920	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1814324	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2230451	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34002293	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34178146	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34181131	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34212866	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34515241	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34591748	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34633582	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34657657	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34661349	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34697113	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34715468	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34767197	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34860428	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34921640	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35158584	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35160541	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35278805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35311230	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35681736	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35903301	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35958032	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35975365	0.91[EUR][1000 genomes]
rs35992154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36078097	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs514438	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55748552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55801120	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60018990	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62019432	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019442	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62020574	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62020575	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62021176	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62021180	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66629206	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71476435	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7168220	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7173383	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7176923	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7177146	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7177892	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7180812	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7181545	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7181634	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181783	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7182292	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7183708	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72707530	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72709850	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72709879	0.83[AMR][1000 genomes]
rs8027748	0.95[AMR][1000 genomes];0.83[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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS 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	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35326382	TUBGCP4	cis	Artery Tibial	GTEx
rs35326382	LCMT2	cis	Esophagus Mucosa	GTEx
rs35326382	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs35326382	TGM7	cis	Esophagus Mucosa	GTEx
rs35326382	ZSCAN29	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623200-43631000	Weak transcription	Lung	lung
2	chr15:43623200-43631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:43623200-43633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:43623200-43651000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:43623200-43651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:43623200-43651600	Weak transcription	Pancreas	Pancrea
7	chr15:43623400-43631200	Weak transcription	Placenta	Placenta
8	chr15:43623400-43632800	Weak transcription	Aorta	Aorta
9	chr15:43623400-43639600	Weak transcription	Fetal Kidney	kidney
10	chr15:43623400-43641200	Weak transcription	Colonic Mucosa	Colon
11	chr15:43623400-43644000	Weak transcription	Fetal Thymus	thymus
12	chr15:43623400-43649200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:43623400-43650400	Weak transcription	Fetal Brain Male	brain
14	chr15:43623400-43651000	Weak transcription	Gastric	stomach
15	chr15:43623400-43651000	Weak transcription	Small Intestine	intestine
16	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:43623600-43631200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr15:43623600-43632200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:43623600-43637800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:43623600-43638000	Weak transcription	Fetal Brain Female	brain
21	chr15:43623600-43642600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr15:43623600-43642600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:43623600-43643200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:43623600-43644000	Weak transcription	Brain Germinal Matrix	brain
25	chr15:43623600-43644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:43623600-43646000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr15:43623600-43646200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:43623600-43646600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr15:43623600-43646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:43623600-43650400	Weak transcription	NH-A	brain
31	chr15:43623600-43650800	Weak transcription	HMEC	breast
32	chr15:43623600-43650800	Weak transcription	NHLF	lung
33	chr15:43623600-43651000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr15:43623600-43651000	Weak transcription	A549	lung
35	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:43623800-43631000	Weak transcription	HSMMtube	muscle
37	chr15:43623800-43631200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:43623800-43631200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:43623800-43633800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr15:43623800-43638000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr15:43623800-43638200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:43623800-43641800	Weak transcription	Psoas Muscle	Psoas
43	chr15:43623800-43645800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:43623800-43646000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:43624000-43633400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:43624000-43641200	Weak transcription	NHEK	skin
47	chr15:43624000-43647000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:43624600-43644600	Weak transcription	Fetal Heart	heart
49	chr15:43625600-43633200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:43625600-43647200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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