Variant report

Variant	rs38729
Chromosome Location	chr7:140703960-140703961
allele	C/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	CEBPB	chr7:140703933-140704094	HepG2	liver:	n/a	chr7:140704050-140704061
2	CEBPB	chr7:140703928-140704092	H1-hESC	embryonic stem cell:	n/a	chr7:140704050-140704061
3	CEBPB	chr7:140703896-140704171	K562	blood:	n/a	chr7:140704050-140704061

No.	Distal block	Cell Line	Cell type
1	chr7:140701133..140705248-chr7:140712773..140716152,4	K562	blood:
2	chr7:140701510..140704472-chr7:140705422..140707944,2	MCF-7	breast:
3	chr7:140700390..140704443-chr7:140712773..140714840,3	K562	blood:
4	chr7:140702442..140704379-chr7:140707606..140710163,3	K562	blood:
5	chr7:140701629..140704089-chr7:140709964..140711981,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BRAF-2	chr7:140702410-140704649	ENSG00000273081.1

Variant related genes	Relation type
CCT4P1	TF binding region
ENSG00000090263	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10271387	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279193	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1089265	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1091374	1.00[ASN][1000 genomes]
rs1091557	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12534351	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534354	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860481	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079829	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246738	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246740	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246741	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246742	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246743	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246744	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246745	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs246746	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2533300	1.00[ASN][1000 genomes]
rs2533307	1.00[ASN][1000 genomes]
rs2533308	1.00[ASN][1000 genomes]
rs2688429	1.00[ASN][1000 genomes]
rs3844322	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38716	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38721	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs38724	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs38725	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38727	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38733	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs38737	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38741	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4020017	1.00[ASN][1000 genomes]
rs4020018	1.00[ASN][1000 genomes]
rs4726134	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62486599	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6949856	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6950813	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71645926	1.00[ASN][1000 genomes]
rs7778860	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7782666	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787917	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs801096	1.00[ASN][1000 genomes]
rs801097	1.00[ASN][1000 genomes]
rs801118	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs801119	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs801122	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs801124	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs801126	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9640306	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017980	chr7:140601863-140721368	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1026448	chr7:140636599-140716829	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs38729	TMEM178B	cis	Esophagus Mucosa	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140698400-140705400	Weak transcription	Fetal Lung	lung
2	chr7:140698600-140713000	Weak transcription	Psoas Muscle	Psoas
3	chr7:140699000-140704000	Enhancers	Fetal Intestine Large	intestine
4	chr7:140699600-140713800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:140700600-140705600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:140701000-140706600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:140701200-140705600	Weak transcription	Small Intestine	intestine
8	chr7:140701400-140713400	Weak transcription	NHLF	lung
9	chr7:140702000-140704800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:140702000-140705200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:140702000-140705400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr7:140702000-140705400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr7:140702000-140707400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:140702000-140709200	Weak transcription	Fetal Kidney	kidney
15	chr7:140702200-140705200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr7:140702200-140705400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:140702200-140705600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:140702400-140705400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:140702400-140705600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:140702600-140705600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:140702800-140713200	Weak transcription	HSMMtube	muscle
22	chr7:140703000-140704800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr7:140703000-140705200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr7:140703000-140705400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:140703000-140705600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr7:140703000-140705600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:140703200-140704800	Weak transcription	Fetal Brain Female	brain
28	chr7:140703200-140704800	Weak transcription	Fetal Muscle Leg	muscle
29	chr7:140703200-140705000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:140703200-140705200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr7:140703200-140705800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr7:140703200-140709400	Weak transcription	HSMM	muscle
33	chr7:140703200-140713800	Weak transcription	Stomach Mucosa	stomach
34	chr7:140703400-140705000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:140703400-140705000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr7:140703400-140705000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr7:140703400-140705200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr7:140703400-140705200	Weak transcription	Brain Hippocampus Middle	brain
39	chr7:140703400-140705200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr7:140703400-140705600	Weak transcription	Left Ventricle	heart
41	chr7:140703400-140705800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:140703400-140705800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:140703400-140706000	Weak transcription	K562	blood
44	chr7:140703400-140713800	Weak transcription	Gastric	stomach
45	chr7:140703600-140704800	Weak transcription	Primary T cells from cord blood	blood
46	chr7:140703600-140705200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr7:140703600-140705200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr7:140703600-140705200	Weak transcription	Aorta	Aorta
49	chr7:140703600-140705200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr7:140703600-140705400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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