Variant report

Variant	rs4253055
Chromosome Location	chr10:50728327-50728328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr10:50728264-50728455	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:50728324-50728623	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:50715711..50718094-chr10:50726640..50728977,2	K562	blood:
2	chr10:50726029..50728979-chr10:50731581..50735350,6	K562	blood:
3	chr10:50727908..50731629-chr10:50735183..50738136,3	MCF-7	breast:
4	chr10:50724821..50729589-chr10:50731335..50734731,5	K562	blood:
5	chr10:50722386..50724704-chr10:50727797..50729912,2	K562	blood:
6	chr10:50728212..50731102-chr10:50742607..50744631,2	K562	blood:
7	chr10:50717666..50720146-chr10:50727918..50729928,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DRGX-3	chr10:50726991-50729600	NONHSAT013309

No data

Variant related genes	Relation type
PGBD3	TF binding region
ENSG00000243251	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1130028	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11812473	0.95[EUR][1000 genomes]
rs11815156	0.88[EUR][1000 genomes]
rs11819019	0.97[EUR][1000 genomes]
rs17010079	0.95[EUR][1000 genomes]
rs17719092	0.90[EUR][1000 genomes]
rs17775180	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2228526	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2228527	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2228529	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs36079558	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4253011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253028	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253101	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4253106	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4253121	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4253165	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4253166	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4253193	1.00[CEU][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs56164647	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs58002245	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs58711755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58912975	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs59898389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61846612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61846615	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61846616	0.98[EUR][1000 genomes]
rs61846617	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61846618	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61846620	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61846637	0.89[EUR][1000 genomes]
rs61850971	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs61850976	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7073830	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7079192	0.90[EUR][1000 genomes]
rs7093098	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7097122	0.89[EUR][1000 genomes]
rs7097866	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7909222	0.90[EUR][1000 genomes]
rs7920256	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs971667	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1051636	chr10:50675292-50732280	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50686600-50731000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr10:50691600-50728400	Weak transcription	Fetal Kidney	kidney
3	chr10:50696400-50731800	Weak transcription	Small Intestine	intestine
4	chr10:50707000-50732200	Weak transcription	NHDF-Ad	bronchial
5	chr10:50707600-50735600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr10:50715000-50732200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:50716200-50731000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:50717200-50729400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr10:50717200-50731200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:50717200-50736200	Weak transcription	Colon Smooth Muscle	Colon
11	chr10:50717200-50746000	Weak transcription	Fetal Heart	heart
12	chr10:50717400-50737000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:50717600-50730600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:50717600-50731600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr10:50718200-50729200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:50720400-50746200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:50721600-50734800	Weak transcription	A549	lung
18	chr10:50721800-50730000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr10:50723000-50729800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr10:50723000-50730000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr10:50723000-50730000	Strong transcription	Primary hematopoietic stem cells	blood
22	chr10:50723000-50734400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:50723000-50741000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:50723200-50741000	Strong transcription	Primary T cells from cord blood	blood
25	chr10:50723200-50741000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:50723200-50741000	Strong transcription	HMEC	breast
27	chr10:50723200-50741800	Strong transcription	Osteobl	bone
28	chr10:50723400-50729200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr10:50723400-50729200	Strong transcription	K562	blood
30	chr10:50723400-50731200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:50723400-50739600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr10:50723400-50741000	Strong transcription	Fetal Intestine Large	intestine
33	chr10:50723400-50741000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr10:50723400-50741600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr10:50723400-50741600	Strong transcription	NHEK	skin
36	chr10:50723600-50741000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:50723800-50731800	Weak transcription	NHLF	lung
38	chr10:50724200-50732200	Weak transcription	Pancreas	Pancrea
39	chr10:50724400-50734800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr10:50724600-50732200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr10:50724800-50731400	Weak transcription	NH-A	brain
42	chr10:50725000-50728400	Weak transcription	Placenta	Placenta
43	chr10:50725000-50746200	Weak transcription	Psoas Muscle	Psoas
44	chr10:50725200-50728600	Weak transcription	Fetal Lung	lung
45	chr10:50725200-50731600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:50725400-50733000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:50725600-50728800	Weak transcription	Primary B cells from cord blood	blood
48	chr10:50725600-50729000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr10:50725600-50731200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:50725600-50731200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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