Variant report

Variant	rs56395939
Chromosome Location	chr4:87963633-87963634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87951686..87953695-chr4:87963099..87965280,2	K562	blood:
2	chr4:87925370..87929364-chr4:87963200..87966939,5	K562	blood:
3	chr4:87963284..87965045-chr4:87965190..87967797,2	K562	blood:
4	chr4:87963142..87968842-chr4:87969641..87976222,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN13-2	chr4:87963228-87963870	NONHSAT097297

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10516788	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471251	0.98[ASN][1000 genomes]
rs17012234	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17012334	0.80[EUR][1000 genomes]
rs17604480	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17701999	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17752307	0.80[ASN][1000 genomes]
rs2061498	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4693801	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55787557	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55816619	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55879154	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55913164	0.80[ASN][1000 genomes]
rs55982755	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56023922	0.82[ASN][1000 genomes]
rs56050898	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56201818	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56390363	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56406125	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6819155	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840258	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6854749	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72667747	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667748	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667750	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72667751	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667752	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667753	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667754	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72667757	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72667759	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72667765	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665282	0.80[ASN][1000 genomes]
rs767315	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682652	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7695426	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87952400-87967000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr4:87952600-87968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:87953400-87965800	Weak transcription	Primary T cells from cord blood	blood
4	chr4:87953400-87967600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:87954600-87965800	Enhancers	Colon Smooth Muscle	Colon
6	chr4:87955600-87964800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr4:87958600-87965800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:87958800-87964200	Weak transcription	Spleen	Spleen
9	chr4:87958800-87968000	Weak transcription	Esophagus	oesophagus
10	chr4:87959200-87967000	Weak transcription	Dnd41	blood
11	chr4:87959400-87966400	Enhancers	Left Ventricle	heart
12	chr4:87959600-87967200	Enhancers	Psoas Muscle	Psoas
13	chr4:87959800-87966000	Weak transcription	Aorta	Aorta
14	chr4:87960000-87964800	Enhancers	Right Atrium	heart
15	chr4:87960400-87964000	Enhancers	GM12878-XiMat	blood
16	chr4:87960400-87964200	Weak transcription	Gastric	stomach
17	chr4:87960400-87965600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:87960400-87965800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:87960400-87968000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:87960400-87975400	Weak transcription	Brain Germinal Matrix	brain
21	chr4:87960600-87964200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:87960600-87965000	Enhancers	Brain Cingulate Gyrus	brain
23	chr4:87960600-87965000	Enhancers	Brain Hippocampus Middle	brain
24	chr4:87960600-87965600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:87960800-87964000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:87960800-87964200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:87960800-87964200	Weak transcription	Fetal Intestine Large	intestine
28	chr4:87960800-87965400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:87960800-87965400	Weak transcription	Fetal Stomach	stomach
30	chr4:87960800-87965400	Weak transcription	NHLF	lung
31	chr4:87960800-87965600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:87960800-87965600	Weak transcription	NH-A	brain
33	chr4:87960800-87965800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:87960800-87966000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr4:87960800-87968000	Weak transcription	HSMM	muscle
36	chr4:87961000-87965000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:87961000-87965200	Weak transcription	NHEK	skin
38	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
39	chr4:87961200-87964600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:87961200-87967800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr4:87961600-87964000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:87961600-87964000	Weak transcription	Fetal Kidney	kidney
43	chr4:87961600-87964400	Weak transcription	Fetal Lung	lung
44	chr4:87961600-87966000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:87961800-87964200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:87961800-87964400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:87961800-87966000	Weak transcription	Thymus	Thymus
48	chr4:87962000-87964800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:87962200-87963800	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr4:87962200-87964600	Enhancers	Primary T cells fromperipheralblood	blood

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