Variant report

Variant	rs72695736
Chromosome Location	chr4:159089720-159089721
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	STAT3	chr4:159089299-159089727	MCF10A-Er-Src	breast:	n/a	chr4:159089368-159089375
2	POLR2A	chr4:159089683-159089877	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:159089656-159090278	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr4:159089656-159089915	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159071408..159073828-chr4:159088522..159091495,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248429	TF binding region
FAM198B	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10517685	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10517686	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11100152	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11933839	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11939690	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036992	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17036995	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17037201	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17037232	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17212066	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17212714	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17271385	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17279270	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881374	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6820988	0.83[EUR][1000 genomes]
rs6834839	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837943	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72691615	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691620	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691622	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691626	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691627	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691629	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691631	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691632	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691633	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691634	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691636	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72691649	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72695726	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72695741	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695744	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695745	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695747	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695748	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695749	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695750	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695751	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72695753	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7678302	0.91[AMR][1000 genomes];0.98[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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs72695736	TMEM144	cis	Esophagus Muscularis	GTEx
rs72695736	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs72695736	FAM198B	cis	Whole Blood	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159076800-159089800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:159078600-159094000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:159083000-159091800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:159083200-159089800	Weak transcription	Fetal Kidney	kidney
5	chr4:159083400-159090400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:159084000-159089800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:159084200-159089800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:159084200-159090000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:159084200-159090800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:159085000-159095200	Active TSS	Aorta	Aorta
11	chr4:159085200-159094000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr4:159085400-159090800	Active TSS	Stomach Smooth Muscle	stomach
13	chr4:159085400-159095000	Active TSS	Right Atrium	heart
14	chr4:159085600-159095000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr4:159086000-159089800	Active TSS	Fetal Muscle Leg	muscle
16	chr4:159086000-159089800	Weak transcription	Pancreas	Pancrea
17	chr4:159086000-159090800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:159086200-159090600	Weak transcription	NH-A	brain
19	chr4:159086200-159091400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:159086400-159090000	Weak transcription	Lung	lung
21	chr4:159086400-159093200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:159087000-159089800	Active TSS	HSMMtube	muscle
23	chr4:159087400-159089800	Genic enhancers	HSMM	muscle
24	chr4:159087400-159091000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:159087600-159089800	Weak transcription	Brain Angular Gyrus	brain
26	chr4:159087600-159090000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr4:159087600-159090200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:159087600-159091800	Active TSS	Ovary	ovary
29	chr4:159087800-159089800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr4:159087800-159090000	Weak transcription	Brain Anterior Caudate	brain
31	chr4:159087800-159090600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:159087800-159090600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:159088000-159091000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr4:159088400-159089800	Active TSS	Left Ventricle	heart
35	chr4:159088400-159091600	Active TSS	Rectal Smooth Muscle	rectum
36	chr4:159088400-159094400	Active TSS	Right Ventricle	heart
37	chr4:159088600-159089800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:159088600-159090600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:159088600-159092000	Active TSS	Brain Hippocampus Middle	brain
40	chr4:159088600-159094400	Active TSS	Fetal Heart	heart
41	chr4:159089000-159089800	Active TSS	Fetal Intestine Large	intestine
42	chr4:159089000-159090000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:159089000-159090400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:159089000-159090400	Active TSS	Muscle Satellite Cultured Cells	--
45	chr4:159089000-159092000	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr4:159089000-159092600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:159089000-159092600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:159089000-159094600	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr4:159089200-159089800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr4:159089200-159089800	Genic enhancers	Osteobl	bone

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