Variant report

Variant	rs12633654
Chromosome Location	chr3:105517328-105517329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10460808	0.82[EUR][1000 genomes]
rs10511246	0.84[ASN][1000 genomes]
rs1075739	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11921710	0.83[ASN][1000 genomes]
rs12635232	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637560	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12637809	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639271	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1561922	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16844736	0.82[EUR][1000 genomes]
rs16851523	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851539	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851563	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851570	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851587	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851630	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867192	0.84[ASN][1000 genomes]
rs1947000	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992521	0.82[EUR][1000 genomes]
rs2089091	0.84[ASN][1000 genomes]
rs2197208	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197209	0.84[ASN][1000 genomes]
rs2301036	0.82[EUR][1000 genomes]
rs57520912	0.83[ASN][1000 genomes]
rs58340800	0.83[ASN][1000 genomes]
rs59534462	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59611997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60295307	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60619938	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437620	0.84[ASN][1000 genomes]
rs6437621	0.84[ASN][1000 genomes]
rs73854891	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73854894	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73857222	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624400	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629357	0.84[ASN][1000 genomes]
rs7648842	0.84[ASN][1000 genomes]
rs9631436	0.83[ASN][1000 genomes]
rs9789988	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826886	0.84[ASN][1000 genomes]
rs9846534	0.84[ASN][1000 genomes]
rs9874600	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
2	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
3	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
4	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
6	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:105505600-105517400	Weak transcription	Brain Substantia Nigra	brain
8	chr3:105506600-105518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:105510000-105517400	Weak transcription	Stomach Mucosa	stomach
11	chr3:105510600-105521200	Weak transcription	Fetal Brain Male	brain
12	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
13	chr3:105511800-105520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:105512000-105520600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:105512200-105517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:105512200-105517400	Weak transcription	Fetal Heart	heart
17	chr3:105512200-105517400	Weak transcription	Ovary	ovary
18	chr3:105512200-105517400	Weak transcription	Small Intestine	intestine
19	chr3:105512200-105519000	Weak transcription	Psoas Muscle	Psoas
20	chr3:105512200-105519000	Weak transcription	Right Atrium	heart
21	chr3:105512200-105519200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:105512200-105520200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:105512200-105520400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
26	chr3:105512400-105524400	Weak transcription	NHLF	lung
27	chr3:105512600-105518200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:105512600-105520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr3:105512600-105524000	Weak transcription	HSMMtube	muscle
30	chr3:105512600-105524600	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:105512600-105525200	Weak transcription	HSMM	muscle
32	chr3:105512800-105517400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:105512800-105517400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:105512800-105517400	Weak transcription	A549	lung
35	chr3:105513400-105517800	Weak transcription	Osteobl	bone
36	chr3:105514000-105517600	Weak transcription	Right Ventricle	heart
37	chr3:105514400-105521600	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:105515200-105518800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr3:105515400-105528200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:105515600-105517400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr3:105515800-105521600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr3:105516000-105518400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:105516000-105519400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr3:105516000-105521600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:105516000-105521600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:105516200-105522200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:105516400-105517400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:105516400-105518400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:105516400-105519400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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