Variant report

Variant	rs72932700
Chromosome Location	chr3:98501845-98501846
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	chr3:98501733-98502061	HepG2	liver:	n/a	n/a
2	EP300	chr3:98501684-98502378	HepG2	liver:	n/a	chr3:98502310-98502324
3	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
4	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
5	NR3C1	chr3:98501741-98502431	ECC-1	luminal epithelium:	n/a	chr3:98502287-98502303 chr3:98502287-98502303 chr3:98502209-98502218
6	NFIC	chr3:98501609-98502143	ECC-1	luminal epithelium:	n/a	n/a
7	EP300	chr3:98501557-98502433	ECC-1	luminal epithelium:	n/a	chr3:98502310-98502324
8	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a
9	TCF12	chr3:98501738-98502403	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10084679	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13317610	0.83[ASN][1000 genomes]
rs13320266	0.83[ASN][1000 genomes]
rs13322253	0.83[ASN][1000 genomes]
rs28417568	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28429424	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28489284	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3796133	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56172805	0.83[ASN][1000 genomes]
rs59906228	0.83[ASN][1000 genomes]
rs72932691	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72934623	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934641	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9810407	0.83[ASN][1000 genomes]
rs9812438	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818215	0.83[ASN][1000 genomes]
rs9833945	0.83[ASN][1000 genomes]
rs9836437	0.83[ASN][1000 genomes]
rs9836915	0.83[ASN][1000 genomes]
rs9838166	0.83[ASN][1000 genomes]
rs9838238	0.83[ASN][1000 genomes]
rs9838706	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839559	0.85[EUR][1000 genomes]
rs9848583	0.83[ASN][1000 genomes]
rs9862660	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870500	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9883751	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
10	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:98494600-98506000	Enhancers	Aorta	Aorta
13	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
15	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
16	chr3:98497400-98503600	Enhancers	Placenta	Placenta
17	chr3:98497600-98502400	Weak transcription	Lung	lung
18	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
19	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
21	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
22	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
23	chr3:98498600-98503000	Weak transcription	Right Atrium	heart
24	chr3:98498800-98502000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:98499000-98503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:98499000-98503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:98499000-98504200	Weak transcription	HSMM	muscle
30	chr3:98499200-98502200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:98499200-98503200	Weak transcription	NHDF-Ad	bronchial
32	chr3:98499200-98503400	Weak transcription	NHLF	lung
33	chr3:98499200-98504200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:98499200-98504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:98499400-98503000	Weak transcription	Fetal Heart	heart
37	chr3:98499400-98503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:98499600-98502000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:98499600-98502000	Weak transcription	Fetal Intestine Large	intestine
41	chr3:98499600-98502200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:98499600-98503000	Weak transcription	Adipose Nuclei	Adipose
43	chr3:98499600-98507800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
45	chr3:98499800-98502200	Weak transcription	Brain Anterior Caudate	brain
46	chr3:98499800-98502200	Weak transcription	Brain Substantia Nigra	brain
47	chr3:98499800-98502800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:98499800-98503200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:98499800-98514800	Weak transcription	Dnd41	blood
50	chr3:98500200-98506000	Enhancers	HMEC	breast

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