Variant report

Variant	rs1976815
Chromosome Location	chr4:57290993-57290994
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:57284634..57287528-chr4:57288727..57291692,2	MCF-7	breast:
2	chr4:57290938..57296949-chr4:57297532..57303755,13	MCF-7	breast:
3	chr4:57289174..57291602-chr4:57330934..57333698,2	MCF-7	breast:
4	chr4:57280047..57284869-chr4:57288459..57291870,6	K562	blood:
5	chr4:57290763..57291840-chr4:57410409..57411390,5	MCF-7	breast:
6	chr4:57290816..57291731-chr4:57301092..57301926,2	K562	blood:
7	chr4:57290807..57291405-chr4:57666039..57666911,2	MCF-7	breast:
8	chr4:57281906..57283505-chr4:57289215..57291492,2	MCF-7	breast:
9	chr4:57275389..57276982-chr4:57289029..57291685,2	K562	blood:
10	chr4:57288977..57293143-chr4:57294508..57297491,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174780	Chromatin interaction
ENSG00000268171	Chromatin interaction
ENSG00000128050	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10031012	0.82[EUR][1000 genomes]
rs10031550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10034154	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11133438	0.80[EUR][1000 genomes]
rs11133439	0.81[EUR][1000 genomes]
rs11724302	0.80[EUR][1000 genomes]
rs11733474	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12331363	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12331412	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13114104	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13133016	0.89[EUR][1000 genomes]
rs13141793	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13147824	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1356788	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401912	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1464286	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474178	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1996650	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030365	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139512	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28559894	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2899063	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3796542	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3796547	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3822003	0.83[EUR][1000 genomes]
rs4167	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4865087	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865100	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865101	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57503982	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59615456	0.81[EUR][1000 genomes]
rs62310633	0.83[EUR][1000 genomes]
rs6554349	0.89[EUR][1000 genomes]
rs6554352	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554355	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6554356	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6812041	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6826795	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6841016	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6841053	0.80[ASN][1000 genomes]
rs6856845	0.81[EUR][1000 genomes]
rs7657711	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661712	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7683781	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7692385	0.88[EUR][1000 genomes]
rs7693683	0.92[EUR][1000 genomes]
rs9312674	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9683679	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9684298	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9997639	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1976815	PPAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
5	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
6	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:57274200-57296400	Weak transcription	Dnd41	blood
8	chr4:57277000-57294200	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:57277000-57299200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:57277000-57300000	Weak transcription	HSMM	muscle
11	chr4:57277800-57298000	Weak transcription	A549	lung
12	chr4:57278000-57291600	Weak transcription	Brain Anterior Caudate	brain
13	chr4:57278000-57291600	Weak transcription	HepG2	liver
14	chr4:57278000-57294000	Weak transcription	HUVEC	blood vessel
15	chr4:57278000-57299200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:57278200-57300200	Weak transcription	Fetal Kidney	kidney
17	chr4:57278200-57300200	Weak transcription	NHDF-Ad	bronchial
18	chr4:57280600-57291800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:57280600-57292600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:57280600-57297800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:57280800-57299400	Weak transcription	Fetal Lung	lung
22	chr4:57281000-57295000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:57281000-57299200	Weak transcription	HMEC	breast
24	chr4:57281600-57291600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:57284000-57294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr4:57284800-57300400	Weak transcription	Fetal Intestine Small	intestine
27	chr4:57286800-57297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:57287800-57291800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:57287800-57291800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:57287800-57299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:57288000-57291000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:57288000-57291000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:57288000-57291200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:57288000-57293000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:57288000-57297800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:57288000-57299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:57289200-57292600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:57289600-57292800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:57289600-57292800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:57289600-57299800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:57290200-57297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:57290400-57291200	Enhancers	Fetal Heart	heart
43	chr4:57290400-57291600	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr4:57290600-57291800	Enhancers	GM12878-XiMat	blood
45	chr4:57290600-57292200	Enhancers	K562	blood
46	chr4:57290800-57291200	Active TSS	Right Atrium	heart
47	chr4:57290800-57291200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr4:57290800-57291400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr4:57290800-57291600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr4:57290800-57291800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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