Variant report

Variant	rs56405245
Chromosome Location	chr3:105495546-105495547
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16851398	1.00[AMR][1000 genomes]
rs16851409	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851417	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851429	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851434	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851455	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851457	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851521	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851530	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851542	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16851606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35835913	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55804660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56323302	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60520841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993723	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72995702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72997617	1.00[AFR][1000 genomes]
rs72997628	1.00[AMR][1000 genomes]
rs7612706	1.00[AMR][1000 genomes]
rs7634544	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
2	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
3	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
4	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:105478800-105496200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
8	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:105481600-105498000	Weak transcription	NH-A	brain
10	chr3:105481800-105507400	Weak transcription	HSMM	muscle
11	chr3:105482000-105496200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:105482000-105496200	Weak transcription	Lung	lung
13	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:105482000-105509600	Weak transcription	Ovary	ovary
16	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
18	chr3:105482400-105500000	Weak transcription	Fetal Stomach	stomach
19	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
20	chr3:105483200-105506200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
22	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
23	chr3:105487000-105497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:105487000-105508400	Weak transcription	Fetal Lung	lung
25	chr3:105487200-105508400	Weak transcription	Fetal Kidney	kidney
26	chr3:105487400-105500600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:105487400-105504200	Weak transcription	Fetal Heart	heart
28	chr3:105489400-105506000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:105489600-105509600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
31	chr3:105489800-105496000	Weak transcription	Right Ventricle	heart
32	chr3:105492400-105495600	Strong transcription	Osteobl	bone
33	chr3:105493000-105501400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:105493000-105501400	Weak transcription	Left Ventricle	heart
35	chr3:105493000-105502400	Weak transcription	Brain Anterior Caudate	brain
36	chr3:105493000-105511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:105493000-105511200	Weak transcription	Right Atrium	heart
38	chr3:105493200-105501400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:105493200-105509000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:105493400-105496400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:105494000-105506200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:105494200-105495800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:105494400-105495600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:105494400-105509400	Weak transcription	Primary B cells from cord blood	blood
45	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:105494600-105495600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:105494600-105495800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:105494800-105495800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:105494800-105495800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:105494800-105496000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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