Variant report

Variant	rs6591226
Chromosome Location	chr11:66675990-66675991
allele	A/C
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	GATA1	chr11:66675550-66676330	PBDE	blood:	n/a	n/a
2	POLR2A	chr11:66675641-66676373	PBDE	blood:	n/a	n/a
3	KAP1	chr11:66675141-66676031	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
PC	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1077256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791896	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227624	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227625	0.85[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs11227628	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227630	0.86[ASN][1000 genomes]
rs1530891	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1901376	0.91[ASN][1000 genomes]
rs34482178	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4483596	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930393	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4930394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67156018	0.89[ASN][1000 genomes]
rs7107498	0.87[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs7110302	0.87[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap]
rs7119682	0.82[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs746018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746019	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936290	0.86[ASN][1000 genomes]
rs7944999	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs7952017	0.91[ASN][1000 genomes]
rs966021	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6591226	FGF4	cis	parietal	SCAN
rs6591226	ACTN3	cis	Muscle Skeletal	GTEx
rs6591226	PC	cis	cerebellum	SCAN
rs6591226	SLC25A45	cis	parietal	SCAN
rs6591226	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs6591226	CDC42BPG	cis	cerebellum	SCAN
rs6591226	EHBP1L1	cis	cerebellum	SCAN
rs6591226	B3GNT1	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66651400-66678400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr11:66671200-66677000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:66671600-66676000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:66672200-66676000	Enhancers	Brain Cingulate Gyrus	brain
5	chr11:66672200-66684000	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr11:66672600-66677200	Enhancers	Brain Substantia Nigra	brain
7	chr11:66672600-66680000	Weak transcription	HUVEC	blood vessel
8	chr11:66672600-66683000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:66672800-66676200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:66673200-66676600	Enhancers	Placenta	Placenta
11	chr11:66673600-66676000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr11:66673600-66676000	Enhancers	Fetal Kidney	kidney
13	chr11:66673600-66676400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr11:66673600-66678000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr11:66673800-66676000	Enhancers	Stomach Mucosa	stomach
16	chr11:66673800-66676200	Enhancers	Ovary	ovary
17	chr11:66673800-66676600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:66674000-66676000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:66674000-66687000	Weak transcription	HSMMtube	muscle
20	chr11:66674200-66676400	Weak transcription	Fetal Brain Female	brain
21	chr11:66674200-66677000	Enhancers	Adipose Nuclei	Adipose
22	chr11:66674200-66677800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:66674200-66679600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:66674200-66680000	Weak transcription	Brain Germinal Matrix	brain
25	chr11:66674400-66677800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:66674400-66677800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:66674400-66679400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:66674400-66679600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:66674400-66679600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:66674400-66679600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:66674400-66679800	Weak transcription	Brain Anterior Caudate	brain
32	chr11:66674400-66689600	Weak transcription	NHLF	lung
33	chr11:66674600-66676000	Weak transcription	Colonic Mucosa	Colon
34	chr11:66674600-66677000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:66674600-66677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:66674600-66678000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr11:66674600-66679600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr11:66674600-66679800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:66674600-66680000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:66674600-66680400	Weak transcription	Right Ventricle	heart
41	chr11:66674600-66684800	Weak transcription	Fetal Stomach	stomach
42	chr11:66674600-66696400	Weak transcription	NHEK	skin
43	chr11:66674800-66676000	Weak transcription	Pancreas	Pancrea
44	chr11:66674800-66677000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:66674800-66679800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:66674800-66680200	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:66675000-66676200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:66675000-66676400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:66675000-66676800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:66675000-66696200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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