Variant report

Variant	rs10270723
Chromosome Location	chr7:108211586-108211587
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	RFX5	chr7:108211070-108211720	K562	blood:	n/a	n/a
2	MAX	chr7:108209197-108211617	K562	blood:	n/a	chr7:108209636-108209645
3	POLR2A	chr7:108208976-108212142	MCF10A-Er-Src	breast:	n/a	n/a
4	JUN	chr7:108208251-108211889	K562	blood:	n/a	n/a
5	HCFC1	chr7:108209080-108211919	Hela-S3	cervix:	n/a	n/a
6	TBL1XR1	chr7:108210752-108211682	K562	blood:	n/a	n/a
7	BHLHE40	chr7:108208641-108211651	K562	blood:	n/a	chr7:108209635-108209648
8	POLR2A	chr7:108209032-108211612	Hela-S3	cervix:	n/a	n/a
9	ZC3H11A	chr7:108209510-108211635	K562	blood:	n/a	n/a
10	POLR2A	chr7:108199426-108221976	K562	blood:	n/a	n/a
11	EP300	chr7:108209495-108211589	K562	blood:	n/a	chr7:108210856-108210872
12	JUND	chr7:108209229-108211618	K562	blood:	n/a	n/a
13	MXI1	chr7:108207302-108212533	SK-N-SH	brain:	n/a	n/a
14	IRF1	chr7:108210823-108212174	K562	blood:	n/a	chr7:108212006-108212020 chr7:108211827-108211841 chr7:108212010-108212020 chr7:108212003-108212015 chr7:108212010-108212024
15	POLR2A	chr7:108209111-108211595	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:108208446-108211787	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr7:108209087-108211746	GM18505	blood:	n/a	n/a
18	IRF1	chr7:108208908-108212102	K562	blood:	n/a	chr7:108212006-108212020 chr7:108211827-108211841 chr7:108209590-108209602 chr7:108212010-108212020 chr7:108212003-108212015 chr7:108212010-108212024

No.	Distal block	Cell Line	Cell type
1	chr7:108209770..108211889-chr7:108236149..108239310,3	K562	blood:
2	chr7:108164038..108167949-chr7:108208349..108211666,8	MCF-7	breast:
3	chr7:108191934..108194448-chr7:108210374..108211887,2	K562	blood:
4	chr7:108095582..108097658-chr7:108210312..108212186,2	MCF-7	breast:
5	chr7:108141868..108144556-chr7:108210151..108212215,2	MCF-7	breast:
6	chr17:56735024..56736952-chr7:108209393..108212263,2	MCF-7	breast:
7	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:
8	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
9	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:
10	chr7:108209600..108213665-chr7:112090307..112092525,3	K562	blood:

Variant related genes	Relation type
THAP5	TF binding region
PNPLA8	TF binding region
DNAJB9	TF binding region
ENSG00000006652	Chromatin interaction
ENSG00000091129	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000225647	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10156002	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253210	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10282368	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1043615	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17426315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1860118	0.85[CEU][hapmap]
rs2041003	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072212	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34668718	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40911	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs40913	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs40916	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs40918	0.85[EUR][1000 genomes]
rs40922	0.89[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40927	0.89[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40929	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40930	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40933	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40937	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40943	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730324	0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10270723	DNAJB9	cis	parietal	SCAN
rs10270723	THAP5	cis	lymphoblastoid	seeQTL
rs10270723	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs10270723	THAP5	cis	cerebellum	SCAN
rs10270723	C7orf66	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108207400-108213400	Active TSS	GM12878-XiMat	blood
2	chr7:108207600-108212000	Active TSS	K562	blood
3	chr7:108208400-108211800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:108208400-108212000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr7:108208600-108211600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr7:108208600-108211800	Active TSS	NHDF-Ad	bronchial
7	chr7:108208600-108211800	Active TSS	NHLF	lung
8	chr7:108208600-108212000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr7:108208600-108212400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr7:108208800-108211600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr7:108208800-108211600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:108208800-108211600	Active TSS	HSMM	muscle
13	chr7:108208800-108211800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr7:108208800-108211800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:108208800-108211800	Active TSS	Placenta	Placenta
16	chr7:108208800-108212200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:108208800-108212200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:108208800-108212400	Active TSS	Right Ventricle	heart
19	chr7:108209000-108211600	Active TSS	Liver	Liver
20	chr7:108209000-108211600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:108209000-108211600	Active TSS	HSMMtube	muscle
22	chr7:108209000-108211800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:108209000-108211800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:108209000-108211800	Active TSS	Fetal Kidney	kidney
25	chr7:108209200-108211600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:108209200-108211600	Active TSS	Fetal Muscle Leg	muscle
27	chr7:108209200-108212000	Active TSS	Fetal Intestine Large	intestine
28	chr7:108209200-108212200	Active TSS	Psoas Muscle	Psoas
29	chr7:108209400-108211600	Active TSS	H9 Cell Line	embryonic stem cell
30	chr7:108209400-108211600	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr7:108209400-108211600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:108209400-108211600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr7:108209400-108211600	Active TSS	Colon Smooth Muscle	Colon
34	chr7:108209400-108211600	Active TSS	Thymus	Thymus
35	chr7:108209400-108211800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:108209400-108211800	Active TSS	Stomach Mucosa	stomach
37	chr7:108209400-108212000	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr7:108209400-108212200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:108209400-108212200	Active TSS	Brain Hippocampus Middle	brain
40	chr7:108209400-108212200	Active TSS	Fetal Intestine Small	intestine
41	chr7:108209400-108212200	Active TSS	HMEC	breast
42	chr7:108209400-108213200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr7:108209600-108211600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr7:108209600-108211600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr7:108209600-108211600	Active TSS	Fetal Lung	lung
46	chr7:108209600-108211800	Active TSS	Hela-S3	cervix
47	chr7:108209600-108212000	Active TSS	Fetal Stomach	stomach
48	chr7:108209600-108212200	Active TSS	Duodenum Mucosa	Duodenum
49	chr7:108209800-108211600	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr7:108209800-108211600	Active TSS	Fetal Brain Female	brain

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