Variant report

Variant	rs6759099
Chromosome Location	chr2:97267260-97267261
allele	C/G
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	RCOR1	chr2:97267187-97268537	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:97258239..97260866-chr2:97265002..97267473,2	K562	blood:
2	chr2:97265918..97267525-chr2:97425302..97427317,2	K562	blood:

Variant related genes	Relation type
KANSL3	TF binding region
ENSG00000158158	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10460601	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10685178	0.86[AFR][1000 genomes]
rs11164109	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11677722	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11678174	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11682934	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11691670	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12469420	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12471390	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12477059	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278563	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4907237	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907240	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4907241	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4907242	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907246	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62154845	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62156200	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66727130	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6747149	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6749159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575254	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580048	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7600903	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6759099	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97248400-97283600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:97254800-97271000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:97255000-97267800	Strong transcription	A549	lung
4	chr2:97256200-97282400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:97256600-97274200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:97256600-97283800	Strong transcription	Placenta	Placenta
7	chr2:97256600-97287000	Strong transcription	Dnd41	blood
8	chr2:97256800-97274200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:97257000-97279600	Strong transcription	Fetal Lung	lung
10	chr2:97257400-97267400	Strong transcription	Fetal Intestine Large	intestine
11	chr2:97257400-97272200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:97257400-97272400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:97257400-97273600	Strong transcription	Left Ventricle	heart
14	chr2:97257400-97274000	Strong transcription	Osteobl	bone
15	chr2:97257400-97274200	Strong transcription	HSMMtube	muscle
16	chr2:97257400-97279600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:97257400-97279600	Strong transcription	Primary hematopoietic stem cells	blood
18	chr2:97257400-97279600	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:97257400-97279800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:97257400-97279800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr2:97257400-97280000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:97257400-97280800	Strong transcription	Fetal Muscle Leg	muscle
23	chr2:97257400-97282400	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:97257600-97267600	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr2:97257600-97280800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr2:97257600-97286400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:97257800-97271800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:97257800-97273000	Strong transcription	Adipose Nuclei	Adipose
29	chr2:97257800-97279400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:97257800-97279400	Strong transcription	Brain Germinal Matrix	brain
31	chr2:97257800-97279600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:97257800-97286800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:97258000-97279400	Strong transcription	Ovary	ovary
34	chr2:97258000-97279400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:97258000-97283200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:97258200-97267600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:97258200-97283200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:97258200-97286400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:97258200-97302800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr2:97258400-97272400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:97258400-97272600	Strong transcription	Colon Smooth Muscle	Colon
42	chr2:97258600-97272000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:97258600-97279800	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr2:97258800-97267600	Strong transcription	K562	blood
45	chr2:97258800-97271200	Strong transcription	NHDF-Ad	bronchial
46	chr2:97258800-97271800	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr2:97258800-97279600	Strong transcription	NHLF	lung
48	chr2:97258800-97280000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:97259000-97267400	Strong transcription	HUVEC	blood vessel
50	chr2:97259200-97273800	Strong transcription	HSMM	muscle

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