Variant report

Variant	rs7742807
Chromosome Location	chr6:4909437-4909438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4897821..4901952-chr6:4908622..4912007,3	MCF-7	breast:
2	chr6:4903747..4905738-chr6:4908891..4910683,2	K562	blood:
3	chr6:4907717..4910185-chr6:4913859..4916843,2	MCF-7	breast:
4	chr6:4909132..4912021-chr6:4912164..4915211,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1113341	0.92[EUR][1000 genomes]
rs1891046	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3930304	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4144546	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4960047	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4960049	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62384665	0.89[ASN][1000 genomes]
rs6904931	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6924037	0.81[ASN][1000 genomes]
rs7738275	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7738459	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7739834	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7759221	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7770206	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7771387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9378917	0.94[ASN][1000 genomes]
rs9378918	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9378919	0.81[ASN][1000 genomes]
rs9378920	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9392068	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9392641	0.82[ASN][1000 genomes]
rs9405786	0.81[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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7742807	FOXC1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4890600-4913800	Weak transcription	Hela-S3	cervix
2	chr6:4893200-4912600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr6:4893600-4910200	Weak transcription	Esophagus	oesophagus
4	chr6:4893600-4914000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:4895000-4917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:4898800-4910200	Weak transcription	Psoas Muscle	Psoas
7	chr6:4899200-4913000	Weak transcription	Ovary	ovary
8	chr6:4900000-4913600	Weak transcription	Brain Substantia Nigra	brain
9	chr6:4900200-4915200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:4900200-4918800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:4901600-4913400	Strong transcription	Fetal Stomach	stomach
12	chr6:4902000-4918400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:4902400-4910000	Weak transcription	Pancreas	Pancrea
14	chr6:4902400-4910200	Weak transcription	Liver	Liver
15	chr6:4903400-4912600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:4904200-4913800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:4904200-4914400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:4904800-4910600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:4905400-4912800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:4905600-4910400	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:4905800-4931200	Weak transcription	HepG2	liver
22	chr6:4906400-4911000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:4906400-4911000	Enhancers	Stomach Mucosa	stomach
24	chr6:4906600-4910800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:4906800-4912000	Weak transcription	Fetal Brain Female	brain
26	chr6:4906800-4913400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:4906800-4914000	Weak transcription	Fetal Kidney	kidney
28	chr6:4907000-4912800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:4907200-4911600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr6:4907400-4911000	Enhancers	Gastric	stomach
31	chr6:4907400-4914200	Weak transcription	Spleen	Spleen
32	chr6:4907400-4914600	Weak transcription	Fetal Intestine Large	intestine
33	chr6:4907600-4909600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:4907600-4911000	Strong transcription	Fetal Muscle Leg	muscle
35	chr6:4907600-4912800	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:4907600-4913000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:4907600-4915600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:4907600-4925200	Weak transcription	Fetal Heart	heart
39	chr6:4907800-4909600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:4907800-4910400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:4908000-4909600	Enhancers	Colonic Mucosa	Colon
42	chr6:4908000-4910400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:4908000-4935600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:4908200-4913600	Weak transcription	HUVEC	blood vessel
45	chr6:4908200-4917000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:4908200-4934800	Weak transcription	Primary B cells from cord blood	blood
47	chr6:4908400-4911000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr6:4908400-4912400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:4908400-4913600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:4908400-4913600	Weak transcription	Fetal Lung	lung

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