Variant report

Variant	rs4229
Chromosome Location	chr10:856918-856919
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:851217..854668-chr10:856285..859147,3	MCF-7	breast:
2	chr10:854955..857145-chr10:859946..862172,2	MCF-7	breast:
3	chr10:849312..852215-chr10:856422..858320,2	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:49)

rs_ID	r²[population]
rs1000278	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1057303	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1057304	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10752020	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10752021	0.86[CHB][hapmap]
rs10904571	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10904572	0.91[ASN][1000 genomes]
rs10904575	0.82[CHB][hapmap]
rs11253448	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11253449	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11253451	0.93[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11253471	0.86[CHB][hapmap]
rs12243303	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12413052	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12413228	0.85[ASN][1000 genomes]
rs12413763	0.89[ASN][1000 genomes]
rs12573825	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1536338	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1555896	0.81[ASN][1000 genomes]
rs1555897	0.93[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555898	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2148368	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274375	0.82[ASN][1000 genomes]
rs2274376	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2892159	0.96[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35913002	0.84[ASN][1000 genomes]
rs3763722	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4097329	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4362075	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4880743	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs4881532	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4881535	0.88[ASN][1000 genomes]
rs4881537	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4881538	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61831437	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61831439	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7071801	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7077992	0.81[CHB][hapmap]
rs7080989	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7091806	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs748112	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs749297	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs752375	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7703	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7899871	0.85[CHB][hapmap]
rs7913077	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7919815	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9124	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs997615	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
rs4229	LARP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:844600-857400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr10:849600-877800	Strong transcription	Fetal Intestine Small	intestine
3	chr10:850200-857200	Weak transcription	Small Intestine	intestine
4	chr10:850600-859000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:850800-857800	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:850800-862800	Weak transcription	Right Atrium	heart
7	chr10:850800-864800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:850800-877800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:851000-883000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:851200-867000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:851200-872400	Strong transcription	Stomach Smooth Muscle	stomach
12	chr10:851200-877800	Strong transcription	Fetal Stomach	stomach
13	chr10:851400-857800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:851400-858000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:851400-859000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr10:851400-862200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:851400-862800	Strong transcription	Lung	lung
18	chr10:851400-867200	Strong transcription	Placenta	Placenta
19	chr10:851400-878600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:851600-863600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr10:851600-865400	Strong transcription	Pancreas	Pancrea
22	chr10:851600-867200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:851600-872800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:851600-876600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr10:851600-883000	Strong transcription	Fetal Intestine Large	intestine
26	chr10:851600-889800	Strong transcription	Dnd41	blood
27	chr10:851600-890800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr10:851600-895600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr10:851800-865600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:851800-867800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:851800-868000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr10:851800-877800	Strong transcription	Liver	Liver
33	chr10:851800-879000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr10:851800-894000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:851800-895800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr10:852000-868000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:852000-872400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr10:852000-876200	Strong transcription	Ovary	ovary
39	chr10:852000-877200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:852000-882800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr10:852200-864600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:852200-864600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:852200-872800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:852200-877800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr10:852200-956400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr10:852400-858800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:852400-859200	Strong transcription	HSMM	muscle
48	chr10:852400-867200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr10:852400-875600	Strong transcription	Thymus	Thymus
50	chr10:852400-876800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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