Variant report

Variant	rs3772100
Chromosome Location	chr3:98501080-98501081
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	CTCF	chr3:98500980-98501130	HBMEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
3	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
4	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10433438	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10935518	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11716579	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11914715	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11916285	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1440154	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16840260	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16846347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17210963	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17278047	0.92[EUR][1000 genomes]
rs17852693	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1822017	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1827158	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278599	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55650073	0.90[EUR][1000 genomes]
rs55662129	0.93[EUR][1000 genomes]
rs55730510	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55988144	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56075614	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56290036	0.93[EUR][1000 genomes]
rs56322058	0.90[EUR][1000 genomes]
rs6440159	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805605	0.90[EUR][1000 genomes]
rs73136038	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136045	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73136048	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73136057	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73136060	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138004	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73138027	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138030	0.93[EUR][1000 genomes]
rs73138048	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73138053	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73138055	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73138058	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73138063	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73138082	0.90[EUR][1000 genomes]
rs73140009	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7614892	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7644946	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8179927	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
3	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
11	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:98494600-98506000	Enhancers	Aorta	Aorta
14	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
16	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
17	chr3:98497400-98501800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98497400-98503600	Enhancers	Placenta	Placenta
19	chr3:98497600-98502400	Weak transcription	Lung	lung
20	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
21	chr3:98498000-98501800	Weak transcription	Gastric	stomach
22	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
24	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
25	chr3:98498400-98501600	Weak transcription	GM12878-XiMat	blood
26	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
27	chr3:98498600-98503000	Weak transcription	Right Atrium	heart
28	chr3:98498800-98502000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:98499000-98503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:98499000-98503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:98499000-98504200	Weak transcription	HSMM	muscle
34	chr3:98499200-98501200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:98499200-98501200	Weak transcription	Fetal Kidney	kidney
36	chr3:98499200-98501800	Weak transcription	NHEK	skin
37	chr3:98499200-98502200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:98499200-98503200	Weak transcription	NHDF-Ad	bronchial
39	chr3:98499200-98503400	Weak transcription	NHLF	lung
40	chr3:98499200-98504200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:98499200-98504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:98499400-98503000	Weak transcription	Fetal Heart	heart
44	chr3:98499400-98503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:98499600-98501200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:98499600-98501400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:98499600-98501600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:98499600-98502000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:98499600-98502000	Weak transcription	Fetal Intestine Large	intestine

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