Variant report

Variant	rs62153906
Chromosome Location	chr2:97005275-97005276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97005124..97008505-chr2:97011571..97014972,4	K562	blood:
2	chr2:97005219..97008922-chr2:97010120..97013534,4	MCF-7	breast:
3	chr2:96999807..97004328-chr2:97004913..97010440,12	MCF-7	breast:
4	chr2:96929425..96932019-chr2:97003452..97006019,2	K562	blood:
5	chr2:97001319..97003188-chr2:97004515..97006524,3	K562	blood:
6	chr2:97005051..97007971-chr2:97016951..97018906,2	K562	blood:

Variant related genes	Relation type
ENSG00000144021	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000121152	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1044594	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1048675	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11903461	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17420101	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17479466	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17633463	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276648	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2276649	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2279105	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3171927	0.90[ASN][1000 genomes]
rs3214058	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3214063	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3731930	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3731935	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731936	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4907231	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907232	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907307	0.82[AMR][1000 genomes]
rs4907308	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4907309	0.83[AMR][1000 genomes]
rs4907310	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4907311	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907312	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56027554	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56800261	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57406815	0.85[EUR][1000 genomes]
rs58328293	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59966106	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59979953	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153033	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62153034	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62153035	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62153039	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153041	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153898	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153900	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153901	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153902	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153905	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153915	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62153923	0.80[AFR][1000 genomes]
rs6755877	0.81[AMR][1000 genomes]
rs7562544	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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	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
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62153906	AC008268.2	cis	lung	GTEx
rs62153906	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs62153906	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs62153906	AC008268.2	cis	Muscle Skeletal	GTEx
rs62153906	CIAO1	cis	Esophagus Mucosa	GTEx
rs62153906	CIAO1	cis	Whole Blood	GTEx
rs62153906	AC008268.2	cis	Artery Tibial	GTEx
rs62153906	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs62153906	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97001800-97016400	Weak transcription	Spleen	Spleen
2	chr2:97002000-97006200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:97002000-97007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:97002000-97036000	Weak transcription	Gastric	stomach
5	chr2:97002200-97005600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:97002200-97006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:97002200-97007200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:97002200-97008000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:97002200-97018800	Weak transcription	Right Atrium	heart
10	chr2:97002200-97037600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:97002400-97005800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:97002400-97006600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:97002400-97007200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:97002400-97007200	Weak transcription	Fetal Brain Female	brain
15	chr2:97002400-97007200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:97002400-97007400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:97002400-97007400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:97002400-97007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:97002400-97007400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:97002400-97007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:97002400-97012600	Weak transcription	Placenta	Placenta
22	chr2:97002400-97016200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:97002400-97018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:97002600-97005400	Weak transcription	Osteobl	bone
25	chr2:97002600-97005600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:97002600-97006400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:97002600-97007000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:97002600-97007200	Weak transcription	Fetal Stomach	stomach
29	chr2:97002600-97007400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:97002600-97007600	Weak transcription	HSMM	muscle
31	chr2:97002600-97009800	Weak transcription	Fetal Kidney	kidney
32	chr2:97002600-97011800	Weak transcription	Small Intestine	intestine
33	chr2:97002600-97017400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:97002600-97031600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:97002800-97006000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:97002800-97006400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:97002800-97006400	Weak transcription	NH-A	brain
38	chr2:97002800-97006600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:97002800-97006800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:97002800-97006800	Weak transcription	NHLF	lung
41	chr2:97002800-97007000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:97002800-97007200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:97002800-97007200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:97002800-97007200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:97002800-97007400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:97002800-97007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:97002800-97007400	Weak transcription	Fetal Intestine Large	intestine
48	chr2:97002800-97007600	Weak transcription	Fetal Lung	lung
49	chr2:97002800-97007600	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:97002800-97007800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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