Variant report

Variant	rs6993229
Chromosome Location	chr8:64107129-64107130
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	chr8:64078842..64081296-chr8:64104717..64107616,2	MCF-7	breast:
2	chr8:64106160..64109170-chr8:64112814..64116314,3	K562	blood:

Variant related genes	Relation type
ENSG00000185728	Chromatin interaction
ENSG00000270673	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10957277	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11785601	0.82[CHD][hapmap]
rs12677532	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13439842	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1435457	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1435458	0.89[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2217827	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4739067	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7000981	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7002089	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7464	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831342	chr8:64084331-64294941	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6993229	PDE7A	cis	cerebellum	SCAN
rs6993229	TTPA	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:64090000-64108200	Weak transcription	Fetal Heart	heart
2	chr8:64097000-64108200	Weak transcription	Right Atrium	heart
3	chr8:64100000-64108200	Weak transcription	Pancreas	Pancrea
4	chr8:64100000-64118800	Weak transcription	Esophagus	oesophagus
5	chr8:64100200-64108200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:64100200-64108200	Weak transcription	Gastric	stomach
7	chr8:64100400-64107200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:64100400-64112600	Weak transcription	Stomach Mucosa	stomach
9	chr8:64100600-64107600	Weak transcription	Right Ventricle	heart
10	chr8:64100600-64113200	Weak transcription	Hela-S3	cervix
11	chr8:64100600-64122200	Weak transcription	Fetal Kidney	kidney
12	chr8:64100600-64127000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:64100800-64113000	Weak transcription	HSMMtube	muscle
14	chr8:64101000-64108600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:64101200-64107600	Weak transcription	Spleen	Spleen
16	chr8:64101200-64108200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr8:64101200-64117200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:64101400-64108200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr8:64101600-64107200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr8:64101600-64108200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:64101600-64128000	Weak transcription	Colonic Mucosa	Colon
22	chr8:64101600-64136000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:64102200-64112400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr8:64102400-64107200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:64102400-64108000	Weak transcription	Fetal Brain Male	brain
26	chr8:64103400-64107400	Weak transcription	Fetal Intestine Small	intestine
27	chr8:64103400-64108200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr8:64103400-64111800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr8:64103400-64115800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr8:64103400-64119800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:64103400-64127400	Weak transcription	Thymus	Thymus
32	chr8:64103600-64107200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr8:64103600-64108200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:64103600-64108400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr8:64103600-64111800	Weak transcription	HepG2	liver
36	chr8:64103600-64112600	Weak transcription	Brain Hippocampus Middle	brain
37	chr8:64103600-64115000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr8:64103600-64119800	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr8:64103600-64120600	Weak transcription	Dnd41	blood
40	chr8:64103600-64121400	Weak transcription	Fetal Thymus	thymus
41	chr8:64103600-64122200	Weak transcription	Placenta	Placenta
42	chr8:64103600-64129800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr8:64103800-64107200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr8:64103800-64108600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr8:64104000-64111800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr8:64104200-64107800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr8:64104200-64111800	Weak transcription	Fetal Intestine Large	intestine
48	chr8:64104400-64124800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr8:64104800-64109400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:64105000-64107400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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