Variant report

Variant	rs13340526
Chromosome Location	chr7:56035308-56035309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:56034811..56036725-chr7:56042594..56044102,2	K562	blood:
2	chr7:56034331..56037104-chr7:56116413..56119304,2	K562	blood:
3	chr7:56035043..56037543-chr7:56067785..56069353,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146733	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10257154	0.82[ASN][1000 genomes]
rs11489729	0.92[AFR][1000 genomes]
rs13222500	0.87[EUR][1000 genomes]
rs13222893	0.82[EUR][1000 genomes]
rs13223226	0.81[ASN][1000 genomes]
rs13232723	0.82[EUR][1000 genomes]
rs13232756	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13236894	0.86[EUR][1000 genomes]
rs13238152	0.84[EUR][1000 genomes]
rs13238424	0.89[EUR][1000 genomes]
rs13239795	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13241227	0.84[EUR][1000 genomes]
rs13243725	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242510	0.89[EUR][1000 genomes]
rs28498258	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34015089	0.87[EUR][1000 genomes]
rs34057777	0.86[EUR][1000 genomes]
rs34114241	0.84[EUR][1000 genomes]
rs34287940	0.84[EUR][1000 genomes]
rs34304703	0.91[EUR][1000 genomes]
rs34372667	0.86[EUR][1000 genomes]
rs34667212	0.84[EUR][1000 genomes]
rs34719181	0.87[EUR][1000 genomes]
rs34719521	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34874704	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35092795	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35160834	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35208675	0.82[EUR][1000 genomes]
rs35210477	0.84[EUR][1000 genomes]
rs35304280	0.82[EUR][1000 genomes]
rs35307785	0.89[EUR][1000 genomes]
rs35551160	0.84[EUR][1000 genomes]
rs35704704	0.84[EUR][1000 genomes]
rs35811559	0.82[EUR][1000 genomes]
rs3735066	0.89[EUR][1000 genomes]
rs3813504	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4360246	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56917729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60007968	0.90[AFR][1000 genomes]
rs71543770	0.87[EUR][1000 genomes]
rs71543773	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71543784	0.89[EUR][1000 genomes]
rs71543785	0.89[EUR][1000 genomes]
rs73343714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73343719	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924900	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers 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	64 gene(s)	inside rSNPs	diseases
8	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription 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	68 gene(s)	inside rSNPs	diseases
11	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' 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
rs13340526	PSPH	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033000-56039200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:56033200-56035400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:56033200-56036200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:56033200-56036800	Weak transcription	Ovary	ovary
5	chr7:56033200-56045400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:56033200-56045600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:56033200-56045600	Weak transcription	Aorta	Aorta
8	chr7:56033200-56045800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:56033200-56048600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:56033200-56050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:56033400-56040400	Weak transcription	Small Intestine	intestine
13	chr7:56033400-56045200	Weak transcription	HUVEC	blood vessel
14	chr7:56033400-56045600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:56033400-56045600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:56033400-56047000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr7:56033400-56047600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:56033600-56036000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:56033600-56036800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:56033600-56037800	Weak transcription	Primary B cells from cord blood	blood
21	chr7:56033600-56045600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr7:56033800-56035400	Enhancers	Lung	lung
23	chr7:56033800-56036400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr7:56033800-56036400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:56033800-56036800	Weak transcription	Primary T cells from cord blood	blood
26	chr7:56033800-56037200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr7:56033800-56038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:56033800-56038400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:56033800-56038400	Weak transcription	HSMMtube	muscle
30	chr7:56033800-56038600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:56033800-56038600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:56033800-56038600	Weak transcription	Stomach Mucosa	stomach
33	chr7:56033800-56039000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:56033800-56039400	Strong transcription	Fetal Intestine Small	intestine
35	chr7:56033800-56045400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:56033800-56045400	Weak transcription	Hela-S3	cervix
37	chr7:56033800-56045400	Weak transcription	HSMM	muscle
38	chr7:56033800-56045600	Weak transcription	Placenta	Placenta
39	chr7:56033800-56045800	Weak transcription	Fetal Thymus	thymus
40	chr7:56033800-56045800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:56033800-56046000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:56033800-56046800	Weak transcription	GM12878-XiMat	blood
43	chr7:56033800-56046800	Weak transcription	NHLF	lung
44	chr7:56033800-56047200	Weak transcription	Colonic Mucosa	Colon
45	chr7:56033800-56047800	Weak transcription	HMEC	breast
46	chr7:56033800-56063000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:56033800-56065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:56034000-56035800	Strong transcription	A549	lung
49	chr7:56034000-56036200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr7:56034000-56036400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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