Variant report

Variant	rs62153029
Chromosome Location	chr2:96920993-96920994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96870008..96876069-chr2:96918284..96921014,6	K562	blood:
2	chr2:96916333..96921176-chr2:96924112..96927591,7	MCF-7	breast:
3	chr2:96870008..96877169-chr2:96918284..96921014,6	K562	blood:
4	chr2:96919042..96921310-chr2:96922215..96923771,2	K562	blood:
5	chr2:96919917..96922377-chr2:96930776..96933155,2	K562	blood:

Variant related genes	Relation type
ENSG00000135956	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000144021	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11551400	0.85[EUR][1000 genomes]
rs12613263	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12617019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12618133	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276650	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3852673	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4371393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4592891	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4826	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57476471	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59082429	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59664047	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60409279	0.80[EUR][1000 genomes]
rs62153010	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62153011	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62153014	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153018	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62153020	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62153022	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72825854	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72825856	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72825864	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72825877	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579709	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7580178	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs997548	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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
rs62153029	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96912200-96922400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:96914400-96924800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:96914400-96929800	Strong transcription	Fetal Stomach	stomach
4	chr2:96915200-96921000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:96915200-96921600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:96915200-96922000	Strong transcription	Thymus	Thymus
7	chr2:96915200-96922200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:96915400-96925000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:96916000-96921800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:96916000-96924800	Strong transcription	Fetal Thymus	thymus
11	chr2:96916000-96929400	Strong transcription	Dnd41	blood
12	chr2:96916400-96921800	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:96916600-96922600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr2:96917200-96921600	Strong transcription	NHEK	skin
15	chr2:96917200-96921800	Strong transcription	Fetal Brain Female	brain
16	chr2:96917200-96924200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:96917400-96921000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:96917400-96921600	Strong transcription	GM12878-XiMat	blood
19	chr2:96917400-96929600	Strong transcription	Brain Germinal Matrix	brain
20	chr2:96917600-96921000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:96917600-96921000	Strong transcription	Ovary	ovary
22	chr2:96917600-96921200	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr2:96917600-96921200	Strong transcription	Colonic Mucosa	Colon
24	chr2:96917600-96921200	Strong transcription	K562	blood
25	chr2:96917600-96921800	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:96917600-96921800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:96917600-96922000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:96917600-96922600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:96917600-96923000	Strong transcription	Gastric	stomach
30	chr2:96917600-96923800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr2:96917600-96924800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:96917600-96925600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:96917800-96921200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:96917800-96921200	Genic enhancers	Liver	Liver
35	chr2:96917800-96921200	Strong transcription	Colon Smooth Muscle	Colon
36	chr2:96917800-96921200	Genic enhancers	Spleen	Spleen
37	chr2:96917800-96921600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:96917800-96921800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:96917800-96921800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:96917800-96921800	Strong transcription	Esophagus	oesophagus
41	chr2:96917800-96921800	Genic enhancers	Left Ventricle	heart
42	chr2:96917800-96925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:96918000-96921000	Strong transcription	Aorta	Aorta
44	chr2:96918000-96921000	Strong transcription	Pancreas	Pancrea
45	chr2:96918000-96921200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr2:96918000-96921200	Genic enhancers	Right Ventricle	heart
47	chr2:96918000-96921600	Strong transcription	Brain Substantia Nigra	brain
48	chr2:96918000-96921800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:96918000-96921800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:96918000-96922400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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