Variant report

Variant	rs34755
Chromosome Location	chr5:96151760-96151761
allele	G/T
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: 55 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs149431	0.97[ASN][1000 genomes]
rs149482	0.88[ASN][1000 genomes]
rs149544	0.97[ASN][1000 genomes]
rs151908	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs151909	0.97[ASN][1000 genomes]
rs151910	0.97[ASN][1000 genomes]
rs151911	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs151953	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs151954	0.97[ASN][1000 genomes]
rs152280	0.83[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs152466	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs187387	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs190298	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs193482	0.97[ASN][1000 genomes]
rs245471	0.87[EUR][1000 genomes]
rs2549805	0.83[YRI][hapmap]
rs26653	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs26654	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs26655	0.82[ASN][1000 genomes]
rs27527	0.86[ASN][1000 genomes]
rs27645	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28129	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34737	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34750	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs34751	0.82[ASN][1000 genomes]
rs34752	0.81[ASN][1000 genomes]
rs34753	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34756	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34757	0.97[ASN][1000 genomes]
rs34759	0.97[ASN][1000 genomes]
rs34760	0.97[ASN][1000 genomes]
rs34761	0.85[CHB][hapmap]
rs34762	0.97[ASN][1000 genomes]
rs34764	0.96[ASN][1000 genomes]
rs35134	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs40090	0.92[ASN][1000 genomes]
rs40091	0.97[ASN][1000 genomes]
rs40604	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs41135	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs42443	0.97[ASN][1000 genomes]
rs468130	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs695965	0.83[ASN][1000 genomes]
rs709669	0.82[EUR][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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs34755	CHD1	cis	cerebellum	SCAN
rs34755	ST8SIA4	cis	parietal	SCAN
rs34755	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs34755	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs34755	ERAP1	cis	multi-tissue	Pritchard
rs34755	ERAP2	cis	cerebellum	SCAN
rs34755	LRAP	cis	multi-tissue	Pritchard
rs34755	ERAP1	cis	Whole Blood	GTEx
rs34755	C5orf36	cis	parietal	SCAN
rs34755	ERAP2	cis	lymphoblastoid	GTEx
rs34755	ERAP1	cis	lung	GTEx
rs34755	ARTS-1	cis	multi-tissue	Pritchard
rs34755	LNPEP	cis	parietal	SCAN
rs34755	LRAP	cis	normal skin	skin_eQTL
rs34755	ERAP2	cis	lymphoblastoid	seeQTL
rs34755	ERAP2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96144400-96152000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:96144600-96151800	Enhancers	Primary T cells from cord blood	blood
3	chr5:96144600-96151800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:96144600-96152200	Weak transcription	Colonic Mucosa	Colon
5	chr5:96144600-96152800	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:96144600-96152800	Weak transcription	Osteobl	bone
7	chr5:96144600-96156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:96144800-96152200	Weak transcription	Placenta	Placenta
9	chr5:96145600-96151800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr5:96146200-96151800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr5:96147600-96152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:96147800-96152200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:96149000-96152000	Weak transcription	K562	blood
14	chr5:96149000-96152400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:96149600-96151800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:96149600-96152200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr5:96149800-96151800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:96149800-96151800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr5:96149800-96152000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr5:96149800-96152000	Enhancers	Fetal Thymus	thymus
21	chr5:96150000-96152000	Weak transcription	Fetal Intestine Small	intestine
22	chr5:96150000-96152000	Weak transcription	NHEK	skin
23	chr5:96150000-96153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:96150200-96152000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr5:96150400-96159800	Weak transcription	Fetal Intestine Large	intestine
26	chr5:96150600-96152000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr5:96151200-96152000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:96151600-96151800	Enhancers	Primary B cells from cord blood	blood
29	chr5:96151600-96151800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:96151600-96151800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:96151600-96151800	Enhancers	GM12878-XiMat	blood
32	chr5:96151600-96152000	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr5:96151600-96152000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr5:96151600-96152000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr5:96151600-96152000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:96151600-96152000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:96151600-96152000	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr5:96151600-96152200	Enhancers	Primary B cells from peripheral blood	blood
39	chr5:96151600-96152200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:96151600-96153000	Flanking Active TSS	Thymus	Thymus
41	chr5:96151600-96154400	Flanking Active TSS	Dnd41	blood

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