Variant report

Variant	rs2120262
Chromosome Location	chr9:100675976-100675977
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr9:100675647-100675981	MCF10A-Er-Src	breast:	n/a	n/a
2	RCOR1	chr9:100675964-100676052	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:86397392..86400390-chr9:100675486..100677661,2	K562	blood:
2	chr9:100435124..100437467-chr9:100674905..100676458,2	K562	blood:
3	chr9:100662549..100664772-chr9:100675385..100677486,2	K562	blood:
4	chr9:100674231..100678302-chr9:100744904..100747134,4	MCF-7	breast:
5	chr9:100675954..100709047-chr9:100737887..100755543,175	K562	blood:

No data

Variant related genes	Relation type
ENSG00000201830	TF binding region
C9orf156	TF binding region
ENSG00000136938	Chromatin interaction
ENSG00000236896	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1007506	0.80[CHB][hapmap]
rs10115216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10119760	0.81[ASN][1000 genomes]
rs10120412	0.81[ASN][1000 genomes]
rs10122541	0.81[ASN][1000 genomes]
rs10512255	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10512256	1.00[YRI][hapmap]
rs1059003	1.00[YRI][hapmap]
rs10739526	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10760011	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10818175	0.81[ASN][1000 genomes]
rs10818213	0.81[AMR][1000 genomes]
rs10984103	0.81[ASN][1000 genomes]
rs10984195	0.86[CHB][hapmap]
rs10984222	0.90[CHB][hapmap]
rs10984230	0.81[AMR][1000 genomes]
rs10984235	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10984253	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10984311	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs10984377	1.00[YRI][hapmap]
rs10984393	0.82[ASN][1000 genomes]
rs10984424	0.82[CHB][hapmap]
rs10984516	1.00[YRI][hapmap]
rs10984532	1.00[YRI][hapmap]
rs10984545	1.00[YRI][hapmap]
rs12004762	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12006522	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12342417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12343182	0.81[ASN][1000 genomes]
rs12375612	1.00[YRI][hapmap]
rs12550872	0.82[ASN][1000 genomes]
rs13299924	0.81[ASN][1000 genomes]
rs1348387	1.00[YRI][hapmap]
rs1443436	0.81[ASN][1000 genomes]
rs1561957	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1561961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17687621	1.00[YRI][hapmap]
rs1947015	1.00[YRI][hapmap]
rs1955144	0.81[ASN][1000 genomes]
rs1955145	0.81[ASN][1000 genomes]
rs2120264	0.81[ASN][1000 genomes]
rs2282190	0.88[CHB][hapmap]
rs2417575	0.81[ASN][1000 genomes]
rs2417576	0.81[ASN][1000 genomes]
rs3758250	0.90[CHB][hapmap]
rs3808893	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3808895	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs3824495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6478469	0.91[ASN][1000 genomes]
rs6478471	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7022148	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7027221	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7031386	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7032086	0.81[AMR][1000 genomes]
rs7032114	0.91[ASN][1000 genomes]
rs7034249	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7034336	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs7034648	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7036589	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7037175	0.81[ASN][1000 genomes]
rs7037324	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7038998	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7042459	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7044799	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7048255	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72753537	0.82[ASN][1000 genomes]
rs7851498	1.00[YRI][hapmap]
rs7854948	1.00[YRI][hapmap]
rs7860144	0.81[ASN][1000 genomes]
rs7866436	0.91[ASN][1000 genomes]
rs7868534	0.81[ASN][1000 genomes]
rs9299258	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
3	nsv525113	chr9:100669799-100686815	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv3483721	chr9:100675531-100678988	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3483722	chr9:100675531-100678988	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2120262	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:100665400-100679000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:100665600-100678200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr9:100666600-100676000	Strong transcription	Fetal Intestine Large	intestine
6	chr9:100667200-100679400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:100667200-100684200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:100669600-100678600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr9:100669600-100678800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
10	chr9:100669800-100676400	Strong transcription	K562	blood
11	chr9:100669800-100678400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:100670000-100676200	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr9:100670000-100678600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr9:100670000-100684200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:100670200-100678600	Strong transcription	Liver	Liver
16	chr9:100670200-100678600	Strong transcription	Placenta	Placenta
17	chr9:100670200-100678600	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr9:100670400-100677000	Strong transcription	GM12878-XiMat	blood
19	chr9:100670400-100678400	Strong transcription	Dnd41	blood
20	chr9:100670400-100679400	Strong transcription	Thymus	Thymus
21	chr9:100670600-100676000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:100670800-100684200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:100671000-100676200	Strong transcription	Left Ventricle	heart
24	chr9:100671000-100677400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:100671000-100677800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:100671000-100678400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:100671200-100676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:100671200-100676400	Strong transcription	Brain Angular Gyrus	brain
29	chr9:100671200-100676600	Strong transcription	Adipose Nuclei	Adipose
30	chr9:100671200-100680200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr9:100671400-100676400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr9:100671400-100678800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr9:100671600-100676000	Strong transcription	Fetal Brain Female	brain
34	chr9:100671600-100676200	Strong transcription	Gastric	stomach
35	chr9:100671600-100676200	Strong transcription	Lung	lung
36	chr9:100671600-100676600	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr9:100671600-100678200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:100671600-100678600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr9:100671600-100678600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr9:100671600-100678600	Strong transcription	Fetal Thymus	thymus
41	chr9:100671600-100678800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:100671800-100676200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:100671800-100676400	Strong transcription	Primary hematopoietic stem cells	blood
44	chr9:100671800-100678400	Strong transcription	Primary B cells from cord blood	blood
45	chr9:100671800-100678600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr9:100671800-100680200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:100672000-100676200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr9:100672000-100679800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr9:100672000-100679800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr9:100672200-100678200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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