Variant report

Variant	rs71476435
Chromosome Location	chr15:43777636-43777637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43776347..43778710-chr15:43783063..43784635,2	K562	blood:
2	15:43770785-43782117..15:43792489-43802874	Hela-S3	cervix:
3	chr15:43776347..43779383-chr15:43782753..43785548,3	K562	blood:
4	15:43770785-43782117..15:44080886-44089111	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000140264	Chromatin interaction
ENSG00000242028	Chromatin interaction
ENSG00000221792	Chromatin interaction
ENSG00000067369	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10518812	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12899865	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12900259	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12905220	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12906017	0.96[EUR][1000 genomes]
rs12906481	1.00[EUR][1000 genomes]
rs12907870	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12908460	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911569	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12911740	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12913977	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12914122	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16957680	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16957715	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16957730	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17723479	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17780417	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17780920	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1814324	0.83[EUR][1000 genomes]
rs2230451	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34002293	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34178146	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34181131	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34212866	0.82[EUR][1000 genomes]
rs34388946	0.89[EUR][1000 genomes]
rs34515241	0.83[EUR][1000 genomes]
rs34591748	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34633582	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34657657	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34661349	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34697113	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34767197	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34860428	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34921640	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35158584	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35160541	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35278805	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35311230	0.81[AFR][1000 genomes]
rs35326382	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35681736	0.83[EUR][1000 genomes]
rs35903301	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35958032	1.00[EUR][1000 genomes]
rs35992154	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36078097	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3862138	0.90[EUR][1000 genomes]
rs514438	0.84[EUR][1000 genomes]
rs55748552	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55801120	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57728767	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs57938858	0.86[EUR][1000 genomes]
rs60018990	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs60367691	0.89[EUR][1000 genomes]
rs62019432	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62020574	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62020575	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62020612	0.89[EUR][1000 genomes]
rs62020616	0.88[EUR][1000 genomes]
rs62021176	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62021180	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66629206	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7173383	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7176923	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7177146	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7177892	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7180812	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7181545	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7181634	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7181783	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182292	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7183708	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72707530	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72709850	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72709879	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8027748	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[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	nsv94676	chr15:43774977-43777774	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs71476435	TUBGCP4	cis	Artery Tibial	GTEx
rs71476435	TGM7	cis	Esophagus Mucosa	GTEx
rs71476435	LCMT2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43734200-43780000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:43734200-43780200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:43744000-43783000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:43744000-43784000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:43746400-43782800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:43749200-43784600	Weak transcription	Stomach Mucosa	stomach
7	chr15:43749400-43783800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:43749400-43784400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:43759600-43779800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:43760400-43784600	Weak transcription	Psoas Muscle	Psoas
11	chr15:43763400-43783800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:43764200-43784400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr15:43766400-43784000	Weak transcription	Spleen	Spleen
14	chr15:43766600-43778800	Strong transcription	NH-A	brain
15	chr15:43767000-43784400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:43767200-43783800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:43767800-43784400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:43767800-43784400	Weak transcription	Colonic Mucosa	Colon
19	chr15:43767800-43784400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr15:43769000-43784400	Weak transcription	Small Intestine	intestine
21	chr15:43770800-43779800	Weak transcription	Fetal Heart	heart
22	chr15:43771200-43779600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr15:43771200-43783800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:43771400-43779600	Weak transcription	Right Ventricle	heart
25	chr15:43771800-43780600	Weak transcription	A549	lung
26	chr15:43771800-43783200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:43772000-43781400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:43772000-43784400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:43772000-43784400	Weak transcription	NHEK	skin
30	chr15:43772200-43780200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr15:43772200-43781200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:43772200-43783800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:43772400-43777800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:43772400-43778800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:43772400-43779400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr15:43772400-43779400	Weak transcription	HUVEC	blood vessel
37	chr15:43772400-43779800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:43772400-43779800	Weak transcription	Aorta	Aorta
39	chr15:43772400-43779800	Weak transcription	Left Ventricle	heart
40	chr15:43772400-43779800	Weak transcription	Thymus	Thymus
41	chr15:43772400-43780000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:43772400-43781400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:43772400-43784000	Weak transcription	Gastric	stomach
44	chr15:43772400-43784000	Weak transcription	GM12878-XiMat	blood
45	chr15:43772400-43784400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:43772400-43784600	Weak transcription	Pancreas	Pancrea
47	chr15:43772600-43778200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:43772600-43778600	Weak transcription	Fetal Thymus	thymus
49	chr15:43772600-43778800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:43772600-43779200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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