Variant report

Variant	rs653673
Chromosome Location	chr11:75202063-75202064
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	FOSL2	chr11:75201598-75202117	SK-N-SH	brain:	n/a	chr11:75201859-75201867 chr11:75201857-75201869
2	NFIC	chr11:75201571-75202063	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr11:75201707-75202068	HUVEC	blood vessel:	n/a	chr11:75201859-75201867 chr11:75201857-75201868 chr11:75201857-75201869
4	FOSL2	chr11:75201710-75202096	A549	lung:	n/a	chr11:75201859-75201867 chr11:75201857-75201869
5	ATF2	chr11:75201668-75202090	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr11:75201667-75202101	H1-hESC	embryonic stem cell:	n/a	chr11:75201859-75201867 chr11:75201857-75201869
7	TEAD4	chr11:75201614-75202148	ECC-1	luminal epithelium:	n/a	n/a
8	SP1	chr11:75201595-75202132	H1-hESC	embryonic stem cell:	n/a	chr11:75201818-75201829
9	TCF12	chr11:75201523-75202290	ECC-1	luminal epithelium:	n/a	n/a
10	JUN	chr11:75201710-75202069	H1-hESC	embryonic stem cell:	n/a	chr11:75201859-75201867 chr11:75201857-75201869
11	JUND	chr11:75201476-75202202	SK-N-SH	brain:	n/a	chr11:75201859-75201867 chr11:75201857-75201869
12	ZBTB7A	chr11:75201561-75202195	ECC-1	luminal epithelium:	n/a	n/a
13	TCF12	chr11:75201490-75202103	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:75189305..75191743-chr11:75201483..75203420,3	K562	blood:

Variant related genes	Relation type
GDPD5	TF binding region
ENSG00000158555	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1004856	0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs10751243	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11236441	0.84[AFR][1000 genomes]
rs1540211	0.80[YRI][hapmap]
rs1557471	0.86[YRI][hapmap]
rs1557474	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623440	0.86[EUR][1000 genomes]
rs1631470	0.89[YRI][hapmap]
rs1631865	0.88[CEU][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790145	0.81[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790149	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790153	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790154	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1790155	0.96[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790156	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1790158	0.92[CEU][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790160	0.86[CEU][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1793396	0.82[JPT][hapmap]
rs1793398	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs1793411	0.81[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1793412	0.88[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1793414	0.89[YRI][hapmap];0.89[AFR][1000 genomes]
rs1793415	0.96[CEU][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1894213	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs471857	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs473462	0.85[EUR][1000 genomes]
rs474056	0.84[EUR][1000 genomes]
rs482458	0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs482503	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs486326	0.84[EUR][1000 genomes]
rs488305	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs492309	0.83[EUR][1000 genomes]
rs504685	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs518611	0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs523617	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532454	0.83[EUR][1000 genomes]
rs535520	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs535523	0.85[EUR][1000 genomes]
rs546632	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs547844	0.85[EUR][1000 genomes]
rs550957	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609793	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611449	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs623338	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs625938	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs628972	0.88[ASW][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs668727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125082	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv825996	chr11:75195626-75203332	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs653673	PLEKHB1	cis	parietal	SCAN
rs653673	ARAP1	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75187200-75203000	Weak transcription	Primary T cells from cord blood	blood
2	chr11:75187400-75202800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr11:75187400-75202800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:75187400-75202800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:75187400-75203000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr11:75190400-75207400	Weak transcription	Fetal Stomach	stomach
7	chr11:75192200-75202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr11:75193000-75203200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr11:75193800-75203200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:75194000-75203000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:75194600-75203000	Weak transcription	Lung	lung
12	chr11:75196400-75202200	Strong transcription	Fetal Intestine Small	intestine
13	chr11:75198200-75203000	Weak transcription	Hela-S3	cervix
14	chr11:75198600-75203600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:75199200-75202800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:75199400-75207000	Weak transcription	Adipose Nuclei	Adipose
17	chr11:75199400-75209800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:75200000-75202600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:75200000-75219600	Weak transcription	Fetal Brain Female	brain
20	chr11:75200200-75203200	Weak transcription	Psoas Muscle	Psoas
21	chr11:75200400-75202400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:75201000-75202200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:75201000-75202400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr11:75201000-75202800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:75201000-75203000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr11:75201000-75203600	Enhancers	Placenta	Placenta
27	chr11:75201000-75203800	Enhancers	HMEC	breast
28	chr11:75201000-75203800	Enhancers	HUVEC	blood vessel
29	chr11:75201200-75202200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:75201200-75202200	Enhancers	HSMM	muscle
31	chr11:75201200-75202600	Enhancers	NH-A	brain
32	chr11:75201200-75203600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:75201200-75203600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:75201200-75203600	Enhancers	A549	lung
35	chr11:75201200-75203800	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr11:75201200-75203800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:75201400-75202200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:75201400-75202200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr11:75201400-75202200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:75201400-75202200	Enhancers	Osteobl	bone
41	chr11:75201400-75202400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:75201400-75202400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr11:75201400-75202400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr11:75201400-75202400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:75201400-75202600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr11:75201400-75202600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:75201400-75203400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:75201400-75203600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:75201400-75203800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr11:75201400-75203800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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