Variant report

Variant	rs340645
Chromosome Location	chr4:87946042-87946043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:87924739..87931529-chr4:87944789..87955863,16	K562	blood:
2	chr4:87940559..87943450-chr4:87945338..87947892,3	K562	blood:
3	chr4:87926504..87929332-chr4:87944740..87946591,3	MCF-7	breast:
4	chr4:87944684..87947564-chr4:87957551..87959550,2	MCF-7	breast:
5	chr4:87945681..87948538-chr4:88025074..88026618,2	MCF-7	breast:
6	chr4:87866229..87868745-chr4:87943992..87946336,2	K562	blood:
7	chr4:87854780..87857653-chr4:87942637..87946103,3	K562	blood:
8	chr4:87944509..87947205-chr4:87948010..87950101,2	K562	blood:
9	chr4:87944178..87948145-chr4:87950244..87953545,6	K562	blood:
10	chr4:87944954..87950016-chr4:87950159..87955839,10	K562	blood:
11	chr4:87926004..87930134-chr4:87942000..87950091,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10003332	0.89[ASN][1000 genomes]
rs10008600	0.92[ASN][1000 genomes]
rs10022960	0.89[ASN][1000 genomes]
rs1374936	0.80[ASN][1000 genomes]
rs1374937	0.80[ASN][1000 genomes]
rs168161	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012291	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972969	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053772	0.92[ASN][1000 genomes]
rs2053774	0.88[ASN][1000 genomes]
rs2272777	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705617	0.80[ASN][1000 genomes]
rs340627	1.00[ASN][1000 genomes]
rs340628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340629	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340631	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340632	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340635	0.97[ASN][1000 genomes]
rs340640	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340644	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs340647	0.95[ASN][1000 genomes]
rs340649	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340652	0.97[ASN][1000 genomes]
rs4536897	0.89[ASN][1000 genomes]
rs4693155	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693797	0.92[ASN][1000 genomes]
rs4693799	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58317309	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6531943	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6531944	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531945	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531947	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815546	0.92[ASN][1000 genomes]
rs6848056	0.90[ASN][1000 genomes]
rs6853011	0.89[ASN][1000 genomes]
rs72876089	0.89[EUR][1000 genomes]
rs73837575	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895740	0.80[ASN][1000 genomes]
rs965824	0.87[ASN][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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 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	chr4:87929400-87946200	Weak transcription	Esophagus	oesophagus
2	chr4:87930600-87946800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:87930600-87950000	Weak transcription	Fetal Stomach	stomach
4	chr4:87931000-87946600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:87935600-87950200	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:87935800-87951000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr4:87936000-87950000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:87937000-87946200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:87937000-87950400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:87937000-87951800	Weak transcription	NHEK	skin
11	chr4:87937000-87952000	Weak transcription	HMEC	breast
12	chr4:87937400-87946200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:87937600-87949800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr4:87939400-87950800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:87939600-87946200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:87939600-87946400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:87939600-87946400	Weak transcription	Brain Angular Gyrus	brain
18	chr4:87939600-87950000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:87939600-87950400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:87939800-87946200	Weak transcription	Pancreas	Pancrea
21	chr4:87940600-87950600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:87940800-87946200	Weak transcription	Fetal Intestine Large	intestine
23	chr4:87940800-87947000	Weak transcription	Fetal Kidney	kidney
24	chr4:87941000-87946200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:87941000-87946200	Weak transcription	Placenta	Placenta
26	chr4:87941000-87946400	Weak transcription	Right Atrium	heart
27	chr4:87941600-87947000	Weak transcription	Dnd41	blood
28	chr4:87941800-87946200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr4:87941800-87947000	Weak transcription	Fetal Thymus	thymus
30	chr4:87942000-87946600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:87942000-87946800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr4:87942200-87946600	Enhancers	Colon Smooth Muscle	Colon
33	chr4:87942600-87947600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:87942600-87950400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:87943000-87947600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:87943000-87948800	Enhancers	Small Intestine	intestine
37	chr4:87943200-87951400	Weak transcription	Fetal Brain Male	brain
38	chr4:87943400-87946200	Weak transcription	Gastric	stomach
39	chr4:87944000-87946400	Enhancers	Stomach Smooth Muscle	stomach
40	chr4:87944000-87949200	Enhancers	Ovary	ovary
41	chr4:87944200-87946200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:87944200-87946600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr4:87944200-87948000	Enhancers	Psoas Muscle	Psoas
44	chr4:87944200-87949000	Enhancers	Liver	Liver
45	chr4:87944200-87951800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr4:87944200-87951800	Enhancers	K562	blood
47	chr4:87944200-87953000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr4:87944200-87960800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:87944400-87948600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr4:87944600-87946800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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