Variant report

Variant	rs34758
Chromosome Location	chr5:96152671-96152672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96142635..96145205-chr5:96151658..96154069,4	MCF-7	breast:
2	chr5:96142184..96145543-chr5:96149000..96152953,5	MCF-7	breast:
3	chr5:96141125..96147304-chr5:96147498..96153496,14	K562	blood:

Variant related genes	Relation type
ENSG00000272109	Chromatin interaction
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12652636	0.90[ASN][1000 genomes]
rs151928	0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs151949	0.92[ASN][1000 genomes]
rs18036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs245478	0.87[CHB][hapmap];0.92[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26613	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26614	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26615	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26616	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26617	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26618	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26650	0.87[CHB][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs26652	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26657	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs27543	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs27778	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28048	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28049	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs469736	0.83[AMR][1000 genomes]
rs469876	0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60432718	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67888194	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv432756	chr5:96113844-96234644	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34758	LRAP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96144600-96152800	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:96144600-96152800	Weak transcription	Osteobl	bone
3	chr5:96144600-96156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:96147600-96152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:96150000-96153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:96150400-96159800	Weak transcription	Fetal Intestine Large	intestine
7	chr5:96151600-96153000	Flanking Active TSS	Thymus	Thymus
8	chr5:96151600-96154400	Flanking Active TSS	Dnd41	blood
9	chr5:96151800-96152800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr5:96151800-96153000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:96151800-96153000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:96151800-96153200	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr5:96151800-96153200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr5:96151800-96153200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr5:96151800-96153600	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr5:96151800-96153600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:96151800-96153600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr5:96151800-96153600	Flanking Active TSS	GM12878-XiMat	blood
19	chr5:96151800-96153800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:96151800-96154200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr5:96152000-96152800	Enhancers	H9 Cell Line	embryonic stem cell
22	chr5:96152000-96152800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr5:96152000-96152800	Active TSS	Duodenum Mucosa	Duodenum
24	chr5:96152000-96153000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr5:96152000-96153000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:96152000-96153000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:96152000-96153000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr5:96152000-96153000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:96152000-96153000	Enhancers	K562	blood
30	chr5:96152000-96153200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr5:96152000-96153200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr5:96152000-96153200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:96152000-96153200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr5:96152000-96153200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:96152000-96153200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:96152000-96153200	Flanking Active TSS	Fetal Thymus	thymus
37	chr5:96152000-96153200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr5:96152200-96152800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:96152200-96152800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:96152200-96153000	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr5:96152200-96153000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr5:96152200-96153000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr5:96152200-96153000	Enhancers	HSMM	muscle
44	chr5:96152200-96153200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr5:96152200-96153600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr5:96152200-96153600	Enhancers	Small Intestine	intestine
47	chr5:96152200-96156600	Weak transcription	NHEK	skin
48	chr5:96152200-96158600	Weak transcription	Spleen	Spleen
49	chr5:96152400-96153000	Active TSS	Colonic Mucosa	Colon
50	chr5:96152400-96153000	Active TSS	Rectal Mucosa Donor 29	rectum

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