Variant report

Variant	rs60520841
Chromosome Location	chr3:105477446-105477447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
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]
rs56405245	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: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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105446600-105477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:105464200-105478200	Weak transcription	Right Atrium	heart
3	chr3:105464800-105482600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:105465600-105478200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:105465800-105483400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:105466000-105481200	Weak transcription	Fetal Kidney	kidney
7	chr3:105466400-105477600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:105466600-105481400	Weak transcription	HepG2	liver
9	chr3:105467600-105478000	Weak transcription	Colonic Mucosa	Colon
10	chr3:105467600-105480800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
12	chr3:105467800-105477600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:105472000-105477800	Weak transcription	Thymus	Thymus
14	chr3:105472200-105477600	Weak transcription	HSMMtube	muscle
15	chr3:105472200-105477800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
17	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
18	chr3:105472600-105478600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:105472800-105480200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:105473000-105477800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr3:105473000-105481400	Weak transcription	NH-A	brain
22	chr3:105473400-105477800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:105473800-105478800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:105474600-105483200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:105474800-105478400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:105475200-105483000	Strong transcription	Osteobl	bone
27	chr3:105475200-105485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:105475400-105478400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:105475600-105477600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:105475600-105478800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:105475800-105483000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:105476000-105486600	Weak transcription	Psoas Muscle	Psoas
33	chr3:105476200-105480400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:105476400-105480400	Weak transcription	Small Intestine	intestine
35	chr3:105476400-105480600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:105476600-105478800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:105477000-105477800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:105477000-105478600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:105477000-105478800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:105477000-105478800	Genic enhancers	Primary T cells from cord blood	blood
41	chr3:105477000-105481200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:105477200-105478800	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr3:105477200-105478800	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr3:105477200-105478800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr3:105477200-105478800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:105477200-105478800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr3:105477200-105478800	ZNF genes & repeats	Esophagus	oesophagus
48	chr3:105477200-105478800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
49	chr3:105477200-105478800	ZNF genes & repeats	Fetal Thymus	thymus
50	chr3:105477200-105478800	Genic enhancers	Left Ventricle	heart

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