Variant report

Variant	rs2276650
Chromosome Location	chr2:96861159-96861160
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	chr2:96860802-96861828	IMR90	lung:	n/a	n/a
2	CEBPB	chr2:96861047-96861430	HepG2	liver:	n/a	n/a
3	CEBPB	chr2:96861030-96861562	IMR90	lung:	n/a	n/a
4	MAFK	chr2:96860542-96861494	IMR90	lung:	n/a	chr2:96861334-96861349
5	POLR2A	chr2:96861053-96861213	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr2:96861014-96861631	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:96861046-96861164	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96856180..96863246-chr2:96870668..96875373,10	MCF-7	breast:

Variant related genes	Relation type
STARD7	TF binding region
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11551400	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs11886999	0.85[CEU][hapmap]
rs12613263	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617019	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12618133	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852673	0.94[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4371393	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4592891	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4826	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57476471	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59082429	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59664047	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153010	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62153011	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153014	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153018	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153020	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62153022	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62153029	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6576968	0.83[CEU][hapmap]
rs72825854	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72825856	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72825864	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72825877	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7579709	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7580178	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs997547	0.83[CEU][hapmap]
rs997548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv3435047	chr2:96836850-96890437	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2276650	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	chr2:96842600-96861600	Weak transcription	Right Atrium	heart
2	chr2:96848600-96861400	Strong transcription	Thymus	Thymus
3	chr2:96848600-96861600	Strong transcription	Fetal Stomach	stomach
4	chr2:96849200-96861400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:96849200-96861400	Strong transcription	Stomach Smooth Muscle	stomach
6	chr2:96849200-96861600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr2:96849400-96861200	Strong transcription	Brain Hippocampus Middle	brain
8	chr2:96849600-96861400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr2:96849600-96861400	Strong transcription	Fetal Thymus	thymus
10	chr2:96849600-96861600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:96849600-96861600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:96849600-96862000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:96849600-96872600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:96849800-96861200	Strong transcription	Liver	Liver
15	chr2:96849800-96861200	Strong transcription	Brain Germinal Matrix	brain
16	chr2:96849800-96861400	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr2:96849800-96861400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:96849800-96861400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:96849800-96861400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:96849800-96861400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:96849800-96861400	Strong transcription	Fetal Brain Female	brain
22	chr2:96849800-96861600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:96849800-96861800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:96849800-96861800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:96849800-96862200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:96849800-96871000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:96850000-96861200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:96850000-96861200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:96850000-96861200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:96850000-96861200	Strong transcription	Brain Cingulate Gyrus	brain
31	chr2:96850000-96861200	Strong transcription	Brain Substantia Nigra	brain
32	chr2:96850000-96861400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:96850000-96861400	Strong transcription	Primary T cells from cord blood	blood
34	chr2:96850000-96861400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:96850000-96861400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:96850000-96861400	Strong transcription	Rectal Smooth Muscle	rectum
37	chr2:96850000-96861400	Strong transcription	Dnd41	blood
38	chr2:96850000-96861600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:96850000-96861600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:96850000-96861600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:96850000-96861800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:96850000-96861800	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:96850000-96862200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:96850000-96862400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:96850200-96861200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr2:96850200-96861400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:96850400-96862000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:96850600-96861200	Strong transcription	Colon Smooth Muscle	Colon
49	chr2:96851000-96869400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:96851200-96861400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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