Variant report

Variant	rs10085823
Chromosome Location	chr7:99009237-99009238
allele	C/T
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	POLR2A	chr7:99008485-99009766	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99008645..99011330-chr7:99036359..99039743,4	K562	blood:
2	chr7:98970407..98975516-chr7:99002028..99009396,17	MCF-7	breast:

Variant related genes	Relation type
PDAP1	TF binding region
BUD31	TF binding region
ENSG00000160917	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10155956	0.86[AMR][1000 genomes]
rs10231948	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10237212	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs10239443	0.86[EUR][1000 genomes]
rs10247946	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs10249659	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10263954	0.86[AMR][1000 genomes]
rs10264303	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10271695	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10277362	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12386578	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13438585	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs14935	1.00[CEU][hapmap]
rs17161650	1.00[MEX][hapmap]
rs28378107	1.00[ASW][hapmap];1.00[CEU][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];1.00[EUR][1000 genomes]
rs28497153	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564953	0.86[EUR][1000 genomes]
rs28655791	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs28754375	0.86[AMR][1000 genomes]
rs3197990	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45529834	1.00[EUR][1000 genomes]
rs45558438	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45599236	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45610838	1.00[EUR][1000 genomes]
rs59463042	0.82[AMR][1000 genomes]
rs60971917	0.82[AMR][1000 genomes]
rs60996680	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61435529	0.86[EUR][1000 genomes]
rs755145	1.00[MEX][hapmap]
rs940334	1.00[CEU][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10085823	STAG3	cis	lymphoblastoid	seeQTL
rs10085823	ATP5J2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99007400-99010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:99007600-99010000	Weak transcription	Ovary	ovary
4	chr7:99007600-99015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:99007800-99012000	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr7:99007800-99024000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:99008000-99009400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
8	chr7:99008000-99009400	Weak transcription	Stomach Mucosa	stomach
9	chr7:99008000-99009600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:99008000-99011200	Strong transcription	Colonic Mucosa	Colon
11	chr7:99008000-99011400	Strong transcription	Aorta	Aorta
12	chr7:99008000-99011600	Strong transcription	Right Ventricle	heart
13	chr7:99008000-99018400	Strong transcription	Gastric	stomach
14	chr7:99008000-99018400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr7:99008000-99019800	Weak transcription	Right Atrium	heart
16	chr7:99008000-99023400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:99008000-99023600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:99008000-99023800	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr7:99008000-99023800	Strong transcription	Placenta	Placenta
20	chr7:99008000-99024000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:99008000-99024000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:99008000-99024000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:99008000-99024000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:99008000-99024000	Strong transcription	Spleen	Spleen
25	chr7:99008000-99024200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr7:99008000-99024200	Strong transcription	Fetal Stomach	stomach
27	chr7:99008000-99026600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:99008200-99009400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr7:99008200-99009600	Genic enhancers	Primary T cells fromperipheralblood	blood
30	chr7:99008200-99010600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:99008200-99011000	Strong transcription	Rectal Smooth Muscle	rectum
32	chr7:99008200-99011200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:99008200-99011400	Strong transcription	HSMM	muscle
34	chr7:99008200-99012400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:99008200-99023400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:99008200-99023600	Strong transcription	Fetal Intestine Large	intestine
37	chr7:99008200-99023800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr7:99008200-99023800	Strong transcription	Fetal Brain Female	brain
39	chr7:99008200-99023800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:99008200-99023800	Strong transcription	Fetal Muscle Leg	muscle
41	chr7:99008200-99024000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr7:99008200-99024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:99008200-99024000	Strong transcription	Lung	lung
44	chr7:99008200-99024200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:99008400-99009400	Strong transcription	Pancreas	Pancrea
46	chr7:99008400-99010800	Strong transcription	Esophagus	oesophagus
47	chr7:99008400-99011000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:99008400-99011200	Strong transcription	Brain Hippocampus Middle	brain
49	chr7:99008400-99011400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr7:99008400-99011400	Strong transcription	Fetal Brain Male	brain

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