Variant report

Variant	rs549034
Chromosome Location	chr11:75203134-75203135
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	GABPA	chr11:75203119-75203642	K562	blood:	n/a	n/a
2	POLR2A	chr11:75203009-75203811	GM12892	blood:	n/a	n/a
3	ZEB1	chr11:75203079-75203505	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:75202996-75203819	GM12892	blood:	n/a	n/a
5	SMARCC1	chr11:75202992-75203774	Hela-S3	cervix:	n/a	chr11:75203420-75203429
6	SPI1	chr11:75203042-75203819	GM12878	blood:	n/a	chr11:75203451-75203460 chr11:75203449-75203462 chr11:75203305-75203318
7	ELF1	chr11:75203055-75203647	GM12878	blood:	n/a	chr11:75203195-75203207 chr11:75203450-75203461 chr11:75203448-75203461

No.	Distal block	Cell Line	Cell type
1	chr11:75189305..75191743-chr11:75201483..75203420,3	K562	blood:
2	chr11:75186423..75188493-chr11:75202325..75205145,2	K562	blood:
3	chr11:75202940..75204464-chr11:75209500..75211854,2	MCF-7	breast:

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1004856	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11236441	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1540210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557471	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1631470	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1783559	1.00[JPT][hapmap]
rs1790144	1.00[JPT][hapmap]
rs1790147	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790152	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793410	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1793414	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2853066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs499613	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544719	0.85[EUR][1000 genomes]
rs548439	0.86[EUR][1000 genomes]
rs550881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571353	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs581007	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628972	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs667410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669601	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75190400-75207400	Weak transcription	Fetal Stomach	stomach
2	chr11:75193000-75203200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:75193800-75203200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:75198600-75203600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr11:75199400-75207000	Weak transcription	Adipose Nuclei	Adipose
6	chr11:75199400-75209800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:75200000-75219600	Weak transcription	Fetal Brain Female	brain
8	chr11:75200200-75203200	Weak transcription	Psoas Muscle	Psoas
9	chr11:75201000-75203600	Enhancers	Placenta	Placenta
10	chr11:75201000-75203800	Enhancers	HMEC	breast
11	chr11:75201000-75203800	Enhancers	HUVEC	blood vessel
12	chr11:75201200-75203600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:75201200-75203600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:75201200-75203600	Enhancers	A549	lung
15	chr11:75201200-75203800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr11:75201200-75203800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:75201400-75203400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:75201400-75203600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:75201400-75203800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr11:75201400-75203800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:75201400-75203800	Enhancers	NHEK	skin
22	chr11:75201400-75207000	Weak transcription	Fetal Intestine Large	intestine
23	chr11:75201600-75203800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:75201600-75204000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:75201800-75203200	Weak transcription	Esophagus	oesophagus
26	chr11:75201800-75204400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr11:75201800-75206800	Weak transcription	HepG2	liver
28	chr11:75202000-75203200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:75202000-75203200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:75202000-75203800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:75202000-75207000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:75202000-75207000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:75202200-75203200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:75202200-75203400	Genic enhancers	Fetal Intestine Small	intestine
35	chr11:75202200-75203800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr11:75202200-75203800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr11:75202200-75207000	Weak transcription	HSMMtube	muscle
38	chr11:75202200-75207200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:75202200-75208800	Weak transcription	HSMM	muscle
40	chr11:75202400-75203400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr11:75202400-75203800	Enhancers	Primary T cells fromperipheralblood	blood
42	chr11:75202400-75203800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr11:75202400-75210000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:75202600-75204200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:75202600-75206800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:75202600-75207000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:75202800-75203200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:75202800-75203200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr11:75202800-75203600	Enhancers	H1 Cell Line	embryonic stem cell
50	chr11:75202800-75203800	Enhancers	Primary B cells from peripheral blood	blood

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