Variant report

Variant	rs1979554
Chromosome Location	chr3:113080851-113080852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10934228	0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11715198	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12488964	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1353903	0.83[CHB][hapmap]
rs1392284	0.87[CHB][hapmap]
rs1463640	0.82[CHB][hapmap]
rs17321330	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1906142	0.90[EUR][1000 genomes]
rs2054823	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2129430	0.81[EUR][1000 genomes]
rs2171293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2895413	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35935366	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682138	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682486	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438140	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438143	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438144	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438145	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438146	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438147	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438148	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66524865	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6768117	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6775574	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6777880	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6805691	0.85[EUR][1000 genomes]
rs7617772	0.85[EUR][1000 genomes]
rs7618884	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621210	0.84[EUR][1000 genomes]
rs7623122	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7623389	0.83[EUR][1000 genomes]
rs7625841	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7631730	0.82[EUR][1000 genomes]
rs7633428	0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7646985	0.80[EUR][1000 genomes]
rs7650538	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs775232	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs775233	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9682734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815835	0.86[EUR][1000 genomes]
rs9840124	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9848087	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9857471	0.83[CHB][hapmap]
rs9866748	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9869141	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9990291	0.82[AMR][1000 genomes];0.81[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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv979867	chr3:113080740-113081353	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1979554	SIDT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113024600-113081000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:113036600-113081000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:113036800-113081000	Weak transcription	Gastric	stomach
4	chr3:113036800-113088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:113042200-113116800	Weak transcription	Primary B cells from cord blood	blood
6	chr3:113042400-113103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:113045400-113097600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:113059000-113081000	Weak transcription	Fetal Stomach	stomach
9	chr3:113066200-113102800	Weak transcription	Aorta	Aorta
10	chr3:113066400-113081000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:113066400-113099000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:113066400-113117600	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:113067600-113094400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:113068400-113117000	Weak transcription	Thymus	Thymus
15	chr3:113069000-113101800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:113069400-113088400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:113069800-113083000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:113070000-113081000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:113070600-113099000	Weak transcription	Adipose Nuclei	Adipose
20	chr3:113070800-113087000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:113071400-113083200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:113072200-113096800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:113072400-113117200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:113072800-113088600	Weak transcription	Spleen	Spleen
25	chr3:113073600-113081000	Weak transcription	Pancreas	Pancrea
26	chr3:113073800-113085400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:113074000-113082000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
29	chr3:113074800-113081000	Weak transcription	Liver	Liver
30	chr3:113077800-113102400	Weak transcription	HSMM	muscle
31	chr3:113078600-113109800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:113079400-113081000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:113079400-113081000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:113079400-113081000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:113079400-113081000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:113079400-113081800	Weak transcription	NHEK	skin
37	chr3:113079800-113081600	Strong transcription	Left Ventricle	heart
38	chr3:113079800-113084200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:113080000-113082600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:113080000-113082600	Weak transcription	HSMMtube	muscle
41	chr3:113080000-113083600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:113080000-113114200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr3:113080000-113123800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:113080200-113081200	Weak transcription	Primary T cells from cord blood	blood
45	chr3:113080200-113082600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:113080200-113085000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:113080200-113117600	Weak transcription	Psoas Muscle	Psoas
48	chr3:113080400-113081600	Strong transcription	Lung	lung
49	chr3:113080600-113081200	Weak transcription	Esophagus	oesophagus
50	chr3:113080800-113081600	Strong transcription	Ovary	ovary

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