Variant report

Variant	rs7752696
Chromosome Location	chr6:53678714-53678715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53678291..53681070-chr6:53681168..53683223,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10498795	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543356	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs16884427	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17748452	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2473603	0.81[AMR][1000 genomes]
rs2820217	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2820218	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3000998	0.85[CHB][hapmap]
rs3799261	1.00[JPT][hapmap]
rs4077760	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4131378	0.84[EUR][1000 genomes]
rs4272222	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4380749	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397225	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580851	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6919924	0.86[EUR][1000 genomes]
rs6925165	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761135	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs9474672	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7752696	TFAP2D	cis	cerebellum	SCAN
rs7752696	LRRC1	cis	parietal	SCAN
rs7752696	FBXO9	cis	parietal	SCAN
rs7752696	COL21A1	cis	cerebellum	SCAN
rs7752696	C6orf142	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
3	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:53668800-53683800	Weak transcription	Ovary	ovary
5	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
11	chr6:53671400-53679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:53673600-53682800	Weak transcription	Dnd41	blood
14	chr6:53674800-53679600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr6:53674800-53680400	Enhancers	Fetal Intestine Small	intestine
16	chr6:53675000-53681200	Weak transcription	Fetal Brain Male	brain
17	chr6:53675400-53679000	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:53675400-53680200	Enhancers	Stomach Mucosa	stomach
19	chr6:53675400-53680400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:53675600-53678800	Enhancers	Hela-S3	cervix
21	chr6:53676200-53678800	Enhancers	Gastric	stomach
22	chr6:53676200-53679200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:53676200-53683600	Weak transcription	Left Ventricle	heart
24	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:53676400-53679200	Weak transcription	Brain Angular Gyrus	brain
26	chr6:53676400-53679800	Weak transcription	Fetal Heart	heart
27	chr6:53676600-53679400	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:53676800-53679800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:53676800-53680000	Weak transcription	Pancreas	Pancrea
30	chr6:53676800-53680400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:53676800-53680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:53676800-53686800	Weak transcription	Right Atrium	heart
33	chr6:53676800-53687200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:53677000-53678800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:53677000-53679600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:53677000-53680000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:53677200-53678800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr6:53677400-53680600	Enhancers	Fetal Intestine Large	intestine
39	chr6:53677600-53680400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:53677600-53680600	Enhancers	Brain Anterior Caudate	brain
41	chr6:53677600-53680600	Enhancers	Small Intestine	intestine
42	chr6:53677600-53680600	Enhancers	HepG2	liver
43	chr6:53677800-53678800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:53677800-53678800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:53677800-53681600	Enhancers	Brain Hippocampus Middle	brain
46	chr6:53678000-53679000	Enhancers	Aorta	Aorta
47	chr6:53678000-53679800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:53678000-53680000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:53678000-53683600	Weak transcription	HMEC	breast
50	chr6:53678200-53680000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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