Variant report

Variant	rs34388946
Chromosome Location	chr15:43829349-43829350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	15:43807815-43812531..15:43825784-43834250	K562	blood:
2	15:43792489-43802874..15:43825784-43834250	K562	blood:
3	chr15:43819879..43821980-chr15:43828096..43830428,2	MCF-7	breast:
4	15:43825784-43834250..15:44067689-44069261	Hela-S3	cervix:
5	15:43825784-43834250..15:44034348-44042259	Hela-S3	cervix:
6	15:43782117-43785993..15:43825784-43834250	Hela-S3	cervix:
7	chr15:43828054..43831995-chr15:43833960..43836416,4	K562	blood:

Variant related genes	Relation type
ENSG00000166963	Chromatin interaction
ENSG00000205771	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000167004	Chromatin interaction
ENSG00000067369	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12899865	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12900259	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12905220	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12906017	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12906481	0.89[EUR][1000 genomes]
rs12907870	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908460	0.81[EUR][1000 genomes]
rs12910639	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12911740	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12913977	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12914122	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16957715	0.81[EUR][1000 genomes]
rs16957730	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17727853	0.80[AMR][1000 genomes]
rs2230451	0.81[EUR][1000 genomes]
rs34002293	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34181131	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34633582	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34661349	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34697113	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34860428	0.82[EUR][1000 genomes]
rs34921640	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35903301	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35958032	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36078097	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3862138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55801120	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56246169	0.80[AMR][1000 genomes]
rs57728767	0.81[EUR][1000 genomes]
rs57938858	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60018990	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60367691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020574	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62020575	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62020612	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62020616	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62021180	0.81[EUR][1000 genomes]
rs66629206	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71476435	0.89[EUR][1000 genomes]
rs7173383	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7177146	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181783	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7182292	0.89[EUR][1000 genomes]
rs72709850	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72709879	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8027748	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8038068	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	nsv428304	chr15:43823158-44008580	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
8	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
10	nsv428633	chr15:43823160-44008580	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34388946	TUBGCP4	cis	Artery Tibial	GTEx
rs34388946	TGM7	cis	Esophagus Mucosa	GTEx
rs34388946	LCMT2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43812000-43844400	Weak transcription	Fetal Brain Male	brain
2	chr15:43815400-43833600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:43815800-43839400	Weak transcription	Stomach Mucosa	stomach
4	chr15:43818000-43835400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:43818000-43852600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr15:43818200-43851600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:43822800-43842800	Weak transcription	HSMM	muscle
8	chr15:43823000-43830200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:43823200-43830000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:43823200-43835600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:43823600-43837400	Weak transcription	Fetal Lung	lung
12	chr15:43823600-43840000	Weak transcription	Psoas Muscle	Psoas
13	chr15:43823800-43833200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:43823800-43836400	Weak transcription	NHLF	lung
15	chr15:43823800-43852600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr15:43824000-43830000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:43824200-43833400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:43824200-43842800	Weak transcription	HSMMtube	muscle
19	chr15:43824200-43845000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:43824400-43830000	Weak transcription	NHDF-Ad	bronchial
21	chr15:43824800-43853000	Weak transcription	GM12878-XiMat	blood
22	chr15:43824800-43853200	Weak transcription	Hela-S3	cervix
23	chr15:43825200-43830000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:43826000-43829400	Strong transcription	Fetal Intestine Large	intestine
25	chr15:43826000-43832000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:43827200-43849800	Weak transcription	Colonic Mucosa	Colon
27	chr15:43827400-43829600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:43827400-43830800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:43827400-43831400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:43827400-43834200	Weak transcription	Fetal Brain Female	brain
31	chr15:43827400-43839800	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:43827400-43841400	Weak transcription	NHEK	skin
33	chr15:43827400-43842400	Weak transcription	Osteobl	bone
34	chr15:43827400-43852600	Weak transcription	Left Ventricle	heart
35	chr15:43827400-43854000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:43827600-43829400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:43827600-43829800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:43827600-43830800	Weak transcription	Fetal Intestine Small	intestine
39	chr15:43827600-43834200	Weak transcription	Dnd41	blood
40	chr15:43827600-43837000	Weak transcription	Gastric	stomach
41	chr15:43827600-43839200	Weak transcription	Primary T cells from cord blood	blood
42	chr15:43827600-43839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:43827600-43840400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:43827600-43840400	Weak transcription	Fetal Stomach	stomach
45	chr15:43827600-43846800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:43827600-43848400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:43827600-43848600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:43827600-43849000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:43827600-43849400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:43827600-43851200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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