Variant report

Variant	rs61539616
Chromosome Location	chr3:140961330-140961331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140960420..140963104-chr3:140988791..140990296,2	K562	blood:
2	chr3:140949314..140952650-chr3:140959989..140963598,3	MCF-7	breast:
3	chr3:140960166..140963166-chr3:140967948..140970939,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs16851210	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16851215	1.00[EUR][1000 genomes]
rs16851264	1.00[EUR][1000 genomes]
rs61710141	1.00[EUR][1000 genomes]
rs6773280	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6779202	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72982504	1.00[EUR][1000 genomes]
rs72982505	1.00[EUR][1000 genomes]
rs72982506	1.00[EUR][1000 genomes]
rs72982513	1.00[EUR][1000 genomes]
rs72982515	1.00[EUR][1000 genomes]
rs72982516	1.00[EUR][1000 genomes]
rs72982519	1.00[EUR][1000 genomes]
rs72994972	1.00[EUR][1000 genomes]
rs73869568	1.00[EUR][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	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:140951800-140962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:140951800-140962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:140952000-140962000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:140955000-140961800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:140955200-140962000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:140955400-140968400	Genic enhancers	Dnd41	blood
9	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:140956200-140962600	Enhancers	Fetal Brain Male	brain
11	chr3:140956400-140962600	Genic enhancers	Thymus	Thymus
12	chr3:140956600-140962600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr3:140956600-140962600	Enhancers	Fetal Muscle Leg	muscle
14	chr3:140956600-140962600	Enhancers	Left Ventricle	heart
15	chr3:140957000-140961800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:140957000-140962200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:140957400-140961800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:140957400-140962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:140957400-140967800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:140957400-140967800	Weak transcription	Gastric	stomach
21	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:140957600-140961600	Enhancers	Fetal Brain Female	brain
23	chr3:140957600-140961800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:140957800-140961800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:140957800-140962000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:140957800-140973600	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:140958000-140962600	Enhancers	Right Atrium	heart
28	chr3:140958200-140961400	Enhancers	Brain Cingulate Gyrus	brain
29	chr3:140958400-140962000	Enhancers	Brain Anterior Caudate	brain
30	chr3:140958400-140962200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:140958600-140961800	Enhancers	Fetal Stomach	stomach
32	chr3:140958600-140962200	Enhancers	Lung	lung
33	chr3:140958600-140962400	Enhancers	Psoas Muscle	Psoas
34	chr3:140958800-140962200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:140958800-140962400	Enhancers	Osteobl	bone
36	chr3:140959000-140961400	Enhancers	Placenta	Placenta
37	chr3:140959000-140962200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:140959000-140962200	Enhancers	NHEK	skin
39	chr3:140959000-140962600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:140959000-140962600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:140959000-140962600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:140959000-140962600	Enhancers	NH-A	brain
43	chr3:140959200-140961400	Weak transcription	Primary T cells from cord blood	blood
44	chr3:140959200-140961400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:140959200-140961400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:140959200-140962000	Enhancers	HSMM	muscle
47	chr3:140959200-140962400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:140959200-140962600	Enhancers	Fetal Muscle Trunk	muscle
49	chr3:140959200-140966200	Enhancers	Fetal Heart	heart
50	chr3:140959200-140998400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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