Variant report

Variant	rs56029850
Chromosome Location	chr1:247364329-247364330
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247336789..247339124-chr1:247364118..247365695,2	K562	blood:

Variant related genes	Relation type
ENSG00000224014	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10924964	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1115202	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567626	0.83[EUR][1000 genomes]
rs12569042	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17269923	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2380117	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892054	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35229190	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3738443	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41315860	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4269806	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4351686	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551629	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4582838	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55643126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55914345	0.88[EUR][1000 genomes]
rs56046175	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56065612	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56340510	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58405512	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60240280	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60698393	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61839991	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61839994	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839996	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839997	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61840000	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61840048	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61840053	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61840054	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61840055	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61840056	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61840057	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61840059	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6656425	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660351	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6665647	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666543	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6668154	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680197	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6684181	0.95[ASN][1000 genomes]
rs6698690	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74152976	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7536883	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546908	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551871	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers 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	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
13	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a
14	nsv873437	chr1:247340784-247366380	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	n/a
15	nsv873438	chr1:247347971-247366380	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	n/a
16	nsv945439	chr1:247362491-247364849	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56029850	RP11-488L18.10	cis	Adipose Subcutaneous	GTEx
rs56029850	RP11-488L18.10	cis	lung	GTEx
rs56029850	RP11-488L18.10	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247346000-247370200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:247346000-247371800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr1:247352000-247368200	ZNF genes & repeats	Liver	Liver
5	chr1:247353000-247367200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:247353000-247368000	ZNF genes & repeats	Primary B cells from cord blood	blood
7	chr1:247353000-247370400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:247353400-247372000	ZNF genes & repeats	GM12878-XiMat	blood
9	chr1:247354000-247371000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:247354800-247371200	Weak transcription	Stomach Mucosa	stomach
11	chr1:247354800-247372400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:247354800-247372400	Weak transcription	Right Ventricle	heart
13	chr1:247356000-247367200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:247356000-247367800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:247356000-247372400	Weak transcription	Brain Anterior Caudate	brain
16	chr1:247356000-247372400	Weak transcription	Fetal Brain Male	brain
17	chr1:247356000-247372600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:247356000-247372600	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:247356200-247372400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:247356200-247372400	Weak transcription	Colonic Mucosa	Colon
21	chr1:247356400-247364600	Weak transcription	Aorta	Aorta
22	chr1:247356400-247372400	Weak transcription	Gastric	stomach
23	chr1:247356600-247364400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:247356600-247367800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:247357000-247367400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:247357200-247367000	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:247357200-247370800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr1:247357600-247366200	Strong transcription	Adipose Nuclei	Adipose
29	chr1:247357600-247367800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:247357800-247365400	Weak transcription	Brain Germinal Matrix	brain
31	chr1:247357800-247366400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:247358000-247368000	Strong transcription	Fetal Thymus	thymus
33	chr1:247358400-247372400	Weak transcription	Fetal Heart	heart
34	chr1:247359000-247364400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:247359000-247372600	Weak transcription	Fetal Kidney	kidney
36	chr1:247359200-247364400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:247359200-247364400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:247359200-247367000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:247359600-247367600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:247360000-247364400	Strong transcription	NHDF-Ad	bronchial
41	chr1:247360000-247365600	Strong transcription	Dnd41	blood
42	chr1:247360000-247366000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:247360200-247365400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:247360400-247365800	Strong transcription	HSMMtube	muscle
45	chr1:247360600-247364400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:247360600-247367200	Strong transcription	K562	blood
47	chr1:247360600-247369000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:247360600-247370400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:247360600-247372400	Weak transcription	Fetal Lung	lung
50	chr1:247360600-247372400	Weak transcription	Rectal Smooth Muscle	rectum

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