Variant report

Variant	rs3813504
Chromosome Location	chr7:56030220-56030221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56029660-56030318	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:56028745-56030638	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr7:56029561-56030223	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr7:56029945-56030914	K562	blood:	n/a	n/a
5	POLR2A	chr7:56030050-56030293	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:56018437..56023114-chr7:56029023..56035214,11	K562	blood:
2	chr7:56029925..56033959-chr7:56116899..56121286,8	MCF-7	breast:
3	chr7:56028151..56030249-chr7:56130757..56133326,2	MCF-7	breast:

Variant related genes	Relation type
GBAS	TF binding region
ENSG00000239789	Chromatin interaction
ENSG00000129103	Chromatin interaction
ENSG00000146729	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000146731	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10257154	0.96[ASN][1000 genomes]
rs13222500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13222893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13223226	0.86[ASN][1000 genomes]
rs13232723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13232756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13233754	0.85[CHB][hapmap];1.00[TSI][hapmap]
rs13236894	0.82[EUR][1000 genomes]
rs13238152	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs13238424	1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13239795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13243072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13243725	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13340526	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17172501	0.85[CHB][hapmap];1.00[TSI][hapmap]
rs2242510	1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs28498258	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34015089	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34057777	1.00[CEU][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs34114241	0.94[AMR][1000 genomes]
rs34279655	0.92[CHB][hapmap];1.00[TSI][hapmap]
rs34287940	0.84[ASN][1000 genomes]
rs34304703	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34372667	0.82[EUR][1000 genomes]
rs34719181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34719521	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34874704	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35092795	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35160834	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35208675	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35210477	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap]
rs35304280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35307785	0.84[EUR][1000 genomes]
rs35811559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3735066	1.00[CEU][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes]
rs4360246	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56917729	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71543770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71543773	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71543784	0.84[EUR][1000 genomes]
rs71543785	0.84[EUR][1000 genomes]
rs73343714	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73343719	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs924900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3813504	PSPH	Cis_1M	lymphoblastoid	RTeQTL
rs3813504	SUMF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56020200-56031200	Weak transcription	Brain Substantia Nigra	brain
2	chr7:56020200-56031400	Weak transcription	Small Intestine	intestine
3	chr7:56020200-56031600	Weak transcription	Aorta	Aorta
4	chr7:56020200-56031800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:56020400-56031000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:56020400-56031200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:56020400-56031200	Weak transcription	NHDF-Ad	bronchial
8	chr7:56020400-56031400	Weak transcription	Brain Angular Gyrus	brain
9	chr7:56020400-56031400	Weak transcription	Colonic Mucosa	Colon
10	chr7:56020400-56031400	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:56020400-56031400	Weak transcription	Esophagus	oesophagus
12	chr7:56020400-56031400	Weak transcription	Fetal Kidney	kidney
13	chr7:56020400-56031600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:56020400-56031600	Weak transcription	Psoas Muscle	Psoas
15	chr7:56020400-56031600	Weak transcription	HUVEC	blood vessel
16	chr7:56020400-56031800	Weak transcription	HSMMtube	muscle
17	chr7:56020400-56032600	Weak transcription	Fetal Lung	lung
18	chr7:56020600-56031400	Weak transcription	Primary B cells from cord blood	blood
19	chr7:56020600-56031600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:56020600-56031800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr7:56020800-56031000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:56020800-56031000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:56021000-56031000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr7:56021000-56031000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:56021000-56031400	Weak transcription	Fetal Heart	heart
26	chr7:56021200-56031200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:56021200-56031400	Weak transcription	Fetal Brain Male	brain
28	chr7:56021800-56031400	Weak transcription	Pancreas	Pancrea
29	chr7:56021800-56031600	Weak transcription	NHLF	lung
30	chr7:56022000-56031400	Weak transcription	Placenta	Placenta
31	chr7:56022000-56031600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:56022000-56031600	Weak transcription	Fetal Thymus	thymus
33	chr7:56022000-56031600	Weak transcription	Osteobl	bone
34	chr7:56022200-56030800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:56022200-56031400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr7:56022200-56031600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr7:56022200-56031600	Weak transcription	Left Ventricle	heart
38	chr7:56022200-56031800	Weak transcription	Brain Germinal Matrix	brain
39	chr7:56022600-56031400	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:56022600-56031400	Weak transcription	GM12878-XiMat	blood
41	chr7:56022800-56031200	Weak transcription	Spleen	Spleen
42	chr7:56022800-56031400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:56022800-56031400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:56022800-56031600	Weak transcription	Gastric	stomach
45	chr7:56022800-56031600	Weak transcription	Ovary	ovary
46	chr7:56023000-56031000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:56023000-56031000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:56023000-56031000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr7:56023000-56031000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr7:56023000-56031200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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