Variant report

Variant	rs4894947
Chromosome Location	chr3:105471508-105471509
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1020327	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1025885	1.00[AMR][1000 genomes]
rs1025886	1.00[AMR][1000 genomes]
rs1036877	1.00[AMR][1000 genomes]
rs1039545	1.00[AMR][1000 genomes]
rs10933832	1.00[AMR][1000 genomes]
rs1348348	1.00[AMR][1000 genomes]
rs1443099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1443107	0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503922	1.00[AMR][1000 genomes]
rs1548056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1561920	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1822348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1838045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867428	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1867429	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1963622	1.00[AMR][1000 genomes]
rs1992520	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2197351	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2221379	1.00[AMR][1000 genomes]
rs3862049	1.00[AMR][1000 genomes]
rs4243428	1.00[AMR][1000 genomes]
rs4282093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4613490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894945	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4894959	1.00[AMR][1000 genomes]
rs4894961	1.00[AMR][1000 genomes]
rs6437615	1.00[AMR][1000 genomes]
rs6437617	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs6437625	1.00[AMR][1000 genomes]
rs6765716	1.00[AMR][1000 genomes]
rs6768096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6804286	1.00[AMR][1000 genomes]
rs6805675	1.00[AMR][1000 genomes]
rs7622735	1.00[AMR][1000 genomes]
rs7643647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7649437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9288816	1.00[AMR][1000 genomes]
rs9288819	1.00[AMR][1000 genomes]
rs9288820	1.00[AMR][1000 genomes]
rs976961	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs976962	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809911	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811870	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs981479	1.00[AMR][1000 genomes]
rs9830539	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9831221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9833645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9838768	1.00[AMR][1000 genomes]
rs9859644	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9872290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv877310	chr3:105409321-105495841	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591244	chr3:105438320-105495841	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv877311	chr3:105449986-105493286	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105439000-105471600	Weak transcription	Fetal Brain Male	brain
2	chr3:105439000-105475800	Weak transcription	Esophagus	oesophagus
3	chr3:105439000-105477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:105439000-105477400	Weak transcription	Lung	lung
5	chr3:105439000-105477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:105439200-105477200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:105446600-105477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:105452400-105477400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:105452800-105477400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:105458000-105475600	Weak transcription	Pancreas	Pancrea
11	chr3:105460200-105471600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:105464200-105477400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:105464200-105478200	Weak transcription	Right Atrium	heart
14	chr3:105464400-105477400	Weak transcription	Fetal Lung	lung
15	chr3:105464600-105477400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:105464800-105477400	Weak transcription	Liver	Liver
17	chr3:105464800-105477400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:105464800-105482600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:105465000-105472000	Weak transcription	HUVEC	blood vessel
20	chr3:105465600-105478200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:105465800-105471600	Weak transcription	Gastric	stomach
22	chr3:105465800-105477200	Weak transcription	Fetal Stomach	stomach
23	chr3:105465800-105477400	Weak transcription	Fetal Intestine Large	intestine
24	chr3:105465800-105477400	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:105465800-105477400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:105465800-105483400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:105466000-105471600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:105466000-105477200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:105466000-105477200	Weak transcription	Right Ventricle	heart
30	chr3:105466000-105477400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:105466000-105481200	Weak transcription	Fetal Kidney	kidney
32	chr3:105466200-105477400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:105466400-105471600	Weak transcription	NH-A	brain
34	chr3:105466400-105471600	Weak transcription	NHEK	skin
35	chr3:105466400-105471800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:105466400-105477400	Weak transcription	NHLF	lung
37	chr3:105466400-105477600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:105466600-105481400	Weak transcription	HepG2	liver
39	chr3:105466800-105477000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:105467200-105471800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:105467200-105476600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:105467400-105473200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:105467400-105477400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:105467600-105471600	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:105467600-105475800	Weak transcription	Ovary	ovary
46	chr3:105467600-105477400	Weak transcription	Aorta	Aorta
47	chr3:105467600-105478000	Weak transcription	Colonic Mucosa	Colon
48	chr3:105467600-105480800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
50	chr3:105467800-105471600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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