Variant report

Variant	rs13439842
Chromosome Location	chr8:64131185-64131186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38276879..38278570-chr8:64129569..64132358,2	MCF-7	breast:
2	chr8:64126271..64129345-chr8:64129580..64131759,4	K562	blood:
3	chr8:64079584..64081553-chr8:64130386..64132208,2	MCF-7	breast:
4	chr8:64118944..64121545-chr8:64130698..64132420,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185728	Chromatin interaction
ENSG00000261542	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000270673	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10957277	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11785601	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12677532	0.93[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs1435457	0.93[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1435458	0.81[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2217827	0.93[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2241754	0.82[GIH][hapmap]
rs4739067	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6993229	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]
rs7000981	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7002089	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7464	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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	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
2	nsv890967	chr8:64107847-64454446	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13439842	TTPA	cis	parietal	SCAN
rs13439842	PDE7A	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:64101600-64136000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:64107000-64132000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr8:64108600-64132000	Weak transcription	Lung	lung
4	chr8:64108600-64134000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:64109000-64132000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr8:64113200-64132600	Weak transcription	Aorta	Aorta
7	chr8:64113600-64132600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr8:64113800-64131800	Weak transcription	Hela-S3	cervix
9	chr8:64114600-64131400	Weak transcription	HSMMtube	muscle
10	chr8:64117800-64131800	Weak transcription	NHLF	lung
11	chr8:64117800-64133200	Weak transcription	Fetal Stomach	stomach
12	chr8:64118400-64132600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:64118400-64133000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr8:64118800-64132000	Weak transcription	Small Intestine	intestine
15	chr8:64119000-64132000	Weak transcription	Ovary	ovary
16	chr8:64119000-64132000	Weak transcription	Pancreas	Pancrea
17	chr8:64119000-64132000	Weak transcription	Right Atrium	heart
18	chr8:64119000-64132000	Weak transcription	Spleen	Spleen
19	chr8:64119200-64132600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr8:64119600-64132800	Weak transcription	Colon Smooth Muscle	Colon
21	chr8:64119600-64138800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr8:64120400-64132000	Weak transcription	Adipose Nuclei	Adipose
23	chr8:64121200-64132000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr8:64121600-64131800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:64121600-64132600	Weak transcription	Psoas Muscle	Psoas
26	chr8:64122000-64132600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr8:64122600-64132000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr8:64122600-64138600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr8:64122800-64131600	Weak transcription	NH-A	brain
30	chr8:64122800-64135000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr8:64122800-64135000	Weak transcription	GM12878-XiMat	blood
32	chr8:64122800-64135200	Weak transcription	Fetal Kidney	kidney
33	chr8:64123000-64132000	Weak transcription	Fetal Lung	lung
34	chr8:64123000-64132600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr8:64123000-64132600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr8:64123000-64138200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr8:64123200-64132200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr8:64123200-64133000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr8:64123200-64133000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr8:64123600-64132000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr8:64123600-64132400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr8:64123800-64131200	Weak transcription	HMEC	breast
43	chr8:64123800-64131400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr8:64123800-64132600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr8:64124000-64135000	Weak transcription	Liver	Liver
46	chr8:64124200-64131400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr8:64124400-64131400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr8:64124400-64135000	Weak transcription	Primary B cells from peripheral blood	blood
49	chr8:64124400-64138800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr8:64124600-64132400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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