Variant report

Variant	rs4543497
Chromosome Location	chr7:56047215-56047216
allele	C/T
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	chr7:56047125-56047429	HepG2	liver:	n/a	n/a
2	FAM48A	chr7:56047027-56047227	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56031887..56033611-chr7:56046548..56048449,2	K562	blood:

Variant related genes	Relation type
GBAS	TF binding region
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10223916	0.81[JPT][hapmap]
rs10229446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10230845	0.81[JPT][hapmap]
rs10233558	0.81[JPT][hapmap]
rs10245725	0.94[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10250964	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10252442	0.94[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10266902	0.88[ASN][1000 genomes]
rs10271662	0.94[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10272406	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10277978	0.81[JPT][hapmap]
rs10435504	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238389	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11761352	0.86[JPT][hapmap]
rs11765287	0.86[JPT][hapmap]
rs11765531	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11765577	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13240915	0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs13241866	0.85[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs13245637	0.85[YRI][hapmap]
rs2135116	0.94[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2174461	0.86[JPT][hapmap]
rs28636652	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28678267	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28803557	0.81[JPT][hapmap]
rs28828764	0.94[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34016595	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35844144	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275190	0.88[YRI][hapmap]
rs4470984	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947533	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4947534	0.85[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4948096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948097	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4948099	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4948102	0.85[CHB][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs57153841	0.89[ASN][1000 genomes]
rs57251705	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs60517461	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6593292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593294	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6593297	1.00[ASW][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap]
rs66528253	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6943341	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[ASN][1000 genomes]
rs6954499	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955423	0.85[EUR][1000 genomes]
rs6973917	0.80[EUR][1000 genomes]
rs6978852	0.81[JPT][hapmap]
rs73132854	0.89[ASN][1000 genomes]
rs73132897	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73360358	0.95[ASN][1000 genomes]
rs73360359	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7776550	0.84[EUR][1000 genomes]
rs7779394	0.81[JPT][hapmap]
rs7793921	0.84[ASW][hapmap]
rs7800001	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7811755	0.86[EUR][1000 genomes]
rs9642405	0.80[AFR][1000 genomes];0.89[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4543497	SUMF2	cis	parietal	SCAN
rs4543497	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL
rs4543497	GBAS	cis	lymphoblastoid	seeQTL
rs4543497	GBAS	cis	multi-tissue	Pritchard
rs4543497	GBAS	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033200-56048600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr7:56033200-56050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:56033400-56047600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:56033800-56047800	Weak transcription	HMEC	breast
6	chr7:56033800-56063000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:56033800-56065800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:56039000-56047600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:56039200-56081600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:56039400-56047400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:56039400-56062400	Weak transcription	Stomach Mucosa	stomach
12	chr7:56040800-56048200	Weak transcription	Small Intestine	intestine
13	chr7:56043800-56049800	Strong transcription	Primary B cells from cord blood	blood
14	chr7:56044000-56053200	Strong transcription	Primary T cells from cord blood	blood
15	chr7:56044600-56050600	Weak transcription	Psoas Muscle	Psoas
16	chr7:56045000-56067400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:56045200-56068200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:56045400-56049800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:56045400-56050000	Strong transcription	Hela-S3	cervix
20	chr7:56045400-56051600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:56045400-56054000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr7:56045400-56054000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr7:56045400-56055000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr7:56045400-56057400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:56045400-56057400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr7:56045400-56057600	Strong transcription	Dnd41	blood
27	chr7:56045400-56059200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:56045400-56067000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:56045400-56067000	Strong transcription	Liver	Liver
30	chr7:56045400-56067200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr7:56045400-56067400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:56045600-56048800	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr7:56045600-56049400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr7:56045600-56049800	Strong transcription	Aorta	Aorta
35	chr7:56045600-56051200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:56045600-56051600	Strong transcription	HepG2	liver
37	chr7:56045600-56053000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr7:56045600-56053200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr7:56045600-56053600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr7:56045600-56053800	Strong transcription	Left Ventricle	heart
41	chr7:56045600-56054000	Strong transcription	Placenta	Placenta
42	chr7:56045600-56054400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:56045600-56054400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr7:56045600-56056400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr7:56045600-56056800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:56045600-56057400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:56045600-56057600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:56045600-56062400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:56045600-56066600	Strong transcription	Fetal Stomach	stomach
50	chr7:56045600-56067400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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