Variant report

Variant	rs60499166
Chromosome Location	chr3:52424316-52424317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52310470..52312704-chr3:52421600..52424589,2	MCF-7	breast:
2	chr3:52420658..52423032-chr3:52423266..52424991,2	K562	blood:
3	chr3:52420801..52424667-chr3:52442297..52446214,5	K562	blood:
4	chr3:52028404..52030718-chr3:52423446..52425346,2	K562	blood:

Variant related genes	Relation type
ENSG00000162244	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000114841	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs3890123	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55971019	1.00[AMR][1000 genomes]
rs56898787	1.00[AMR][1000 genomes]
rs56961704	1.00[AMR][1000 genomes]
rs58781613	1.00[AMR][1000 genomes]
rs60997031	1.00[AMR][1000 genomes]
rs61734628	1.00[AMR][1000 genomes]
rs6766038	1.00[AMR][1000 genomes]
rs73835766	1.00[AMR][1000 genomes]
rs73837049	1.00[AMR][1000 genomes]
rs73837599	1.00[AMR][1000 genomes]
rs73838354	1.00[AMR][1000 genomes]
rs73839116	1.00[AMR][1000 genomes]
rs73839117	1.00[AMR][1000 genomes]
rs7638914	1.00[AMR][1000 genomes]
rs7641255	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv590302	chr3:52407933-52428988	Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
3	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
5	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
6	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
8	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
9	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
10	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
14	chr3:52409800-52425200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:52410000-52425200	Weak transcription	Primary B cells from cord blood	blood
16	chr3:52410000-52433200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:52410000-52434400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:52410200-52425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:52410200-52426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:52410600-52424800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:52410600-52425000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr3:52411000-52425200	Weak transcription	Pancreas	Pancrea
24	chr3:52411400-52424800	Weak transcription	Gastric	stomach
25	chr3:52413800-52433000	Weak transcription	Fetal Brain Female	brain
26	chr3:52414000-52433200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:52414000-52435400	Weak transcription	Fetal Lung	lung
28	chr3:52414200-52425000	Weak transcription	Right Ventricle	heart
29	chr3:52414800-52434800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:52416600-52425200	Weak transcription	Esophagus	oesophagus
31	chr3:52418600-52442200	Strong transcription	Fetal Intestine Small	intestine
32	chr3:52418800-52430000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:52418800-52430000	Strong transcription	Brain Cingulate Gyrus	brain
34	chr3:52418800-52430600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:52418800-52441800	Strong transcription	Brain Anterior Caudate	brain
36	chr3:52419000-52425200	Strong transcription	Spleen	Spleen
37	chr3:52419000-52431200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:52419000-52441800	Strong transcription	Liver	Liver
39	chr3:52419000-52442000	Strong transcription	Brain Hippocampus Middle	brain
40	chr3:52419000-52442600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:52419200-52429800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:52419200-52435400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:52419200-52441600	Strong transcription	Fetal Stomach	stomach
44	chr3:52419200-52441800	Strong transcription	Brain Angular Gyrus	brain
45	chr3:52419200-52442000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr3:52419400-52428800	Strong transcription	Primary T cells from cord blood	blood
47	chr3:52419600-52432800	Weak transcription	Fetal Thymus	thymus
48	chr3:52419600-52435600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:52419800-52428000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:52420000-52424400	Weak transcription	Stomach Smooth Muscle	stomach

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