Variant report

Variant	rs1000278
Chromosome Location	chr10:852629-852630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:852322..854745-chr10:858049..860254,2	K562	blood:
2	chr10:851047..854031-chr10:861867..864621,2	K562	blood:
3	chr10:456178..457890-chr10:852622..854288,2	MCF-7	breast:
4	chr10:851217..854668-chr10:856285..859147,3	MCF-7	breast:
5	chr10:851680..853848-chr10:854341..855901,2	K562	blood:
6	chr10:849218..853180-chr10:854145..855910,4	K562	blood:
7	chr10:847643..849814-chr10:851213..852909,2	K562	blood:

Variant related genes	Relation type
ENSG00000107929	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1057303	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1057304	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10752020	0.90[ASN][1000 genomes]
rs10752021	0.82[ASN][1000 genomes]
rs10904571	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10904572	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11253448	0.93[ASN][1000 genomes]
rs11253449	0.93[ASN][1000 genomes]
rs11253451	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12243303	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12413052	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12413228	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12413763	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12573825	0.93[ASN][1000 genomes]
rs12774722	0.80[ASN][1000 genomes]
rs1536338	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1555896	0.86[ASN][1000 genomes]
rs1555897	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1555898	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2148368	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274375	0.88[ASN][1000 genomes]
rs2274376	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2892159	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35913002	0.90[ASN][1000 genomes]
rs3763722	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4097329	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4229	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4362075	0.87[ASN][1000 genomes]
rs4880743	0.86[ASN][1000 genomes]
rs4881532	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4881535	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4881537	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4881538	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61831437	0.90[ASN][1000 genomes]
rs61831439	0.88[ASN][1000 genomes]
rs7071801	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7080989	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7091806	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs748112	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs749297	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs752375	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7703	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7913077	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7919815	0.90[ASN][1000 genomes]
rs9124	0.91[ASN][1000 genomes]
rs997615	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS 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	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1048859	chr10:442805-887622	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1039958	chr10:450753-889167	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
5	nsv540400	chr10:450753-889167	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv549753	chr10:458477-894838	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1044857	chr10:577396-856059	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv540402	chr10:577396-856059	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS 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 miRNA	43 gene(s)	inside rSNPs	diseases
10	nsv948602	chr10:708293-944641	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv949063	chr10:708293-974870	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv894718	chr10:763714-861390	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv1045119	chr10:766867-855251	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1043812	chr10:776547-981126	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv540406	chr10:776547-981126	Bivalent Enhancer Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
19	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv1048707	chr10:834439-915534	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
21	nsv466698	chr10:836115-888073	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
22	nsv549766	chr10:836115-888073	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	nsv5498	chr10:849137-860462	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1000278	LARP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:835600-853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:835800-852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:836000-852800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:836600-853000	Weak transcription	Stomach Mucosa	stomach
5	chr10:839200-852800	Weak transcription	NHDF-Ad	bronchial
6	chr10:843400-852800	Weak transcription	Brain Substantia Nigra	brain
7	chr10:843400-853000	Weak transcription	Aorta	Aorta
8	chr10:843600-852800	Weak transcription	HSMMtube	muscle
9	chr10:844600-857400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr10:846600-853000	Weak transcription	A549	lung
11	chr10:846800-853000	Weak transcription	NHEK	skin
12	chr10:849400-853000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:849400-856400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:849600-852800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr10:849600-877800	Strong transcription	Fetal Intestine Small	intestine
16	chr10:850000-852800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:850000-853800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr10:850200-853000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr10:850200-857200	Weak transcription	Small Intestine	intestine
20	chr10:850400-853000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr10:850400-854400	Weak transcription	Fetal Heart	heart
22	chr10:850400-855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:850600-853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr10:850600-853600	Weak transcription	Primary B cells from cord blood	blood
25	chr10:850600-856000	Strong transcription	Brain Germinal Matrix	brain
26	chr10:850600-856600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:850600-859000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr10:850800-852800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr10:850800-852800	Weak transcription	Fetal Lung	lung
30	chr10:850800-856600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr10:850800-857800	Weak transcription	Colon Smooth Muscle	Colon
32	chr10:850800-862800	Weak transcription	Right Atrium	heart
33	chr10:850800-864800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:850800-877800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:851000-852800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr10:851000-852800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr10:851000-852800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:851000-852800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr10:851000-852800	Weak transcription	Fetal Thymus	thymus
40	chr10:851000-852800	Weak transcription	NH-A	brain
41	chr10:851000-853000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:851000-856600	Strong transcription	Fetal Brain Female	brain
43	chr10:851000-883000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:851200-853000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr10:851200-853000	Weak transcription	Brain Angular Gyrus	brain
46	chr10:851200-853000	Weak transcription	HUVEC	blood vessel
47	chr10:851200-856200	Strong transcription	Gastric	stomach
48	chr10:851200-856600	Strong transcription	Esophagus	oesophagus
49	chr10:851200-856600	Strong transcription	NHLF	lung
50	chr10:851200-867000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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