Variant report

Variant	rs499613
Chromosome Location	chr11:75194485-75194486
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	RAD21	chr11:75194174-75194501	HepG2	liver:	n/a	n/a
2	RCOR1	chr11:75194251-75194535	HepG2	liver:	n/a	n/a
3	HNF4A	chr11:75194159-75194490	HepG2	liver:	n/a	chr11:75194295-75194307 chr11:75194294-75194309
4	HNF4A	chr11:75194126-75194491	HepG2	liver:	n/a	chr11:75194295-75194307 chr11:75194294-75194309
5	HDAC2	chr11:75194009-75194535	HepG2	liver:	n/a	n/a
6	FOXA2	chr11:75194197-75194492	HepG2	liver:	n/a	n/a
7	HNF4A	chr11:75194135-75194632	HepG2	liver:	n/a	chr11:75194295-75194307 chr11:75194294-75194309

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:75191759..75194523-chr11:75195624..75199123,4	K562	blood:
2	chr11:75185809..75187737-chr11:75194465..75195996,2	K562	blood:

Variant related genes	Relation type
GDPD5	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1004856	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs11236441	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1540210	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557471	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1631470	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1790144	0.81[YRI][hapmap]
rs1790147	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790152	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793410	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1793414	0.90[CEU][hapmap];0.97[EUR][1000 genomes]
rs2853066	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504793	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511190	0.84[EUR][1000 genomes]
rs514477	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540269	0.84[EUR][1000 genomes]
rs544719	0.89[EUR][1000 genomes]
rs548439	0.91[EUR][1000 genomes]
rs549034	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]
rs550881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566818	0.84[EUR][1000 genomes]
rs571353	0.91[EUR][1000 genomes]
rs581007	0.95[CEU][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589724	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628972	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs667410	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669601	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682292	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75187000-75194800	Strong transcription	Fetal Intestine Small	intestine
2	chr11:75187000-75201400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:75187200-75201200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr11:75187200-75203000	Weak transcription	Primary T cells from cord blood	blood
5	chr11:75187400-75198200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:75187400-75202800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr11:75187400-75202800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:75187400-75202800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:75187400-75203000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:75187600-75201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:75187600-75202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:75187800-75201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:75188000-75201600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:75188200-75200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:75188400-75201200	Weak transcription	HSMM	muscle
16	chr11:75188400-75201400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:75188400-75201400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:75188400-75201600	Weak transcription	HSMMtube	muscle
19	chr11:75188600-75201600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr11:75190000-75194600	Enhancers	Fetal Muscle Leg	muscle
21	chr11:75190400-75199000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:75190400-75199200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:75190400-75207400	Weak transcription	Fetal Stomach	stomach
24	chr11:75190800-75201600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:75191000-75196800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:75192000-75194600	Enhancers	Pancreas	Pancrea
27	chr11:75192200-75194600	Enhancers	Fetal Muscle Trunk	muscle
28	chr11:75192200-75194600	Enhancers	Right Ventricle	heart
29	chr11:75192200-75202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:75192400-75198200	Weak transcription	Fetal Intestine Large	intestine
31	chr11:75192800-75195000	Enhancers	Spleen	Spleen
32	chr11:75193000-75203200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:75193800-75194600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:75193800-75194600	Enhancers	Lung	lung
35	chr11:75193800-75194800	Enhancers	Adipose Nuclei	Adipose
36	chr11:75193800-75196200	Enhancers	Liver	Liver
37	chr11:75193800-75203200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr11:75194000-75194600	Enhancers	Left Ventricle	heart
39	chr11:75194000-75194600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr11:75194000-75196800	Enhancers	HepG2	liver
41	chr11:75194000-75203000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:75194200-75194600	Enhancers	Placenta	Placenta
43	chr11:75194200-75194800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:75194200-75197200	Weak transcription	Psoas Muscle	Psoas
45	chr11:75194400-75194600	Enhancers	Right Atrium	heart
46	chr11:75194400-75197800	Weak transcription	Brain Germinal Matrix	brain

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