Variant report

Variant	rs55720941
Chromosome Location	chr3:142153196-142153197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142152079..142156407-chr3:142164108..142168187,4	MCF-7	breast:
2	chr3:142150817..142154662-chr3:142162783..142169338,6	MCF-7	breast:
3	chr3:142145904..142149296-chr3:142151128..142153785,4	K562	blood:

Variant related genes	Relation type
ENSG00000114127	Chromatin interaction
ENSG00000242479	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs16852327	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4462984	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55712145	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55810370	0.99[AFR][1000 genomes]
rs56044159	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56791995	1.00[AMR][1000 genomes]
rs58286086	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58978582	1.00[AMR][1000 genomes]
rs59954506	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60153076	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61076760	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61265290	0.87[AMR][1000 genomes]
rs6440079	1.00[AMR][1000 genomes]
rs6440080	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6796807	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6797767	1.00[AMR][1000 genomes]
rs73864538	1.00[AMR][1000 genomes]
rs73864539	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73864541	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73867022	1.00[AMR][1000 genomes]
rs73867024	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73867035	1.00[AMR][1000 genomes]
rs73867040	1.00[AMR][1000 genomes]
rs73867041	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7618139	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv522549	chr3:141812759-142164735	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv523945	chr3:141933649-142219542	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1000083	chr3:141956718-142172666	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv523596	chr3:142132749-142164735	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142083600-142158600	Weak transcription	NHEK	skin
2	chr3:142112200-142154600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:142127400-142159600	Weak transcription	Psoas Muscle	Psoas
4	chr3:142131600-142156000	Weak transcription	Fetal Heart	heart
5	chr3:142136400-142157400	Weak transcription	HMEC	breast
6	chr3:142138600-142158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:142138600-142164600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:142138800-142163000	Weak transcription	Spleen	Spleen
9	chr3:142139400-142156200	Weak transcription	Small Intestine	intestine
10	chr3:142139400-142157000	Weak transcription	Brain Germinal Matrix	brain
11	chr3:142139400-142158600	Weak transcription	Pancreas	Pancrea
12	chr3:142139400-142163200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:142141200-142157000	Weak transcription	Esophagus	oesophagus
14	chr3:142141600-142162400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:142142200-142165400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:142142400-142153400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:142142800-142153200	Weak transcription	HUVEC	blood vessel
18	chr3:142146600-142164200	Weak transcription	Stomach Mucosa	stomach
19	chr3:142149000-142162600	Weak transcription	Brain Substantia Nigra	brain
20	chr3:142149600-142153200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:142149800-142165000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:142150000-142156000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:142150000-142162000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:142150000-142162200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:142150000-142163200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:142150000-142164000	Weak transcription	NHDF-Ad	bronchial
27	chr3:142150000-142164400	Weak transcription	Aorta	Aorta
28	chr3:142150000-142164600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:142150200-142155000	Weak transcription	Fetal Kidney	kidney
30	chr3:142150200-142155400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:142150200-142155400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:142150200-142156200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr3:142150200-142156400	Weak transcription	Fetal Brain Female	brain
34	chr3:142150200-142156400	Weak transcription	NHLF	lung
35	chr3:142150200-142162000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:142150200-142162200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:142150200-142162600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:142150200-142163200	Weak transcription	Colonic Mucosa	Colon
39	chr3:142150200-142164000	Weak transcription	Fetal Brain Male	brain
40	chr3:142150200-142164400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:142150200-142164400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:142150200-142164600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:142150200-142164600	Weak transcription	HSMMtube	muscle
44	chr3:142150400-142153200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:142150400-142154000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:142150400-142154600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:142150400-142155000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:142150400-142156200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:142150400-142158600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:142150400-142158600	Weak transcription	Primary hematopoietic stem cells	blood

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