Variant report

Variant	rs10991900
Chromosome Location	chr9:94119997-94119998
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	NFYB	chr9:94119971-94120178	GM12878	blood:	n/a	chr9:94120105-94120117 chr9:94120106-94120120

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94113397..94115728-chr9:94119035..94121876,2	MCF-7	breast:
2	chr9:94119074..94121011-chr9:94185358..94187790,2	MCF-7	breast:

Variant related genes	Relation type
AUH	TF binding region
ENSG00000165030	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10991848	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10991849	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10991853	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10991880	0.82[EUR][1000 genomes]
rs10991882	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683737	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13289294	0.84[ASN][1000 genomes]
rs1331691	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1397575	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs16907358	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16907394	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1848984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[EUR][1000 genomes]
rs1877125	0.86[EUR][1000 genomes]
rs4480236	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55642352	0.91[EUR][1000 genomes]
rs59727648	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6479337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7019926	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7020893	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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]
rs7028794	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7042178	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7849152	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7852888	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7856089	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs7866204	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7868501	0.86[EUR][1000 genomes]
rs7868771	0.91[CHB][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893570	chr9:93973938-94148084	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482877	chr9:93979351-94157734	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv893571	chr9:94072113-94202927	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10991900	ECM2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94093200-94122600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:94097800-94121600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:94101000-94122400	Weak transcription	HUVEC	blood vessel
4	chr9:94102000-94122400	Weak transcription	HMEC	breast
5	chr9:94104400-94122800	Weak transcription	Colonic Mucosa	Colon
6	chr9:94104600-94121200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:94104600-94121400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr9:94104600-94122000	Weak transcription	Gastric	stomach
9	chr9:94104800-94121200	Weak transcription	Brain Anterior Caudate	brain
10	chr9:94104800-94121400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:94104800-94121400	Weak transcription	Brain Substantia Nigra	brain
12	chr9:94104800-94121800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr9:94104800-94122000	Weak transcription	Spleen	Spleen
14	chr9:94104800-94122400	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr9:94104800-94122400	Weak transcription	NHLF	lung
16	chr9:94104800-94122600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr9:94104800-94122600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr9:94104800-94122600	Weak transcription	HSMMtube	muscle
19	chr9:94104800-94123600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:94105200-94120600	Weak transcription	Fetal Heart	heart
21	chr9:94105200-94121400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:94105200-94121800	Weak transcription	Fetal Brain Male	brain
23	chr9:94105200-94122600	Weak transcription	Osteobl	bone
24	chr9:94105200-94122800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:94105400-94122600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:94105600-94121000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:94105600-94123000	Weak transcription	Placenta	Placenta
28	chr9:94106400-94122800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:94108800-94122000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:94109800-94122600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:94109800-94123000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:94109800-94123000	Weak transcription	Esophagus	oesophagus
33	chr9:94110200-94122400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr9:94111200-94122000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr9:94111600-94120000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr9:94111800-94120000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:94112800-94122200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:94113200-94120000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr9:94113200-94120200	Strong transcription	Liver	Liver
40	chr9:94113600-94122600	Weak transcription	NH-A	brain
41	chr9:94114000-94121800	Weak transcription	Pancreas	Pancrea
42	chr9:94114000-94122600	Weak transcription	Fetal Muscle Leg	muscle
43	chr9:94114200-94121800	Weak transcription	Brain Hippocampus Middle	brain
44	chr9:94114200-94122400	Weak transcription	Fetal Kidney	kidney
45	chr9:94114200-94122400	Weak transcription	A549	lung
46	chr9:94114200-94122600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:94114200-94122800	Weak transcription	Aorta	Aorta
48	chr9:94114400-94121800	Weak transcription	Thymus	Thymus
49	chr9:94114400-94122000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:94114400-94122000	Weak transcription	Rectal Smooth Muscle	rectum

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