Variant report

Variant	rs7562544
Chromosome Location	chr2:97006685-97006686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

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	chr2:96873666..96875672-chr2:97006603..97009131,2	K562	blood:
5	chr2:97006581..97009347-chr2:97011114..97012829,3	MCF-7	breast:
6	chr2:96964603..96966846-chr2:97005907..97008831,2	K562	blood:
7	chr2:97005051..97007971-chr2:97016951..97018906,2	K562	blood:
8	chr2:96999907..97005565-chr2:97005819..97011243,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000121152	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1044594	0.84[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1048675	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11903461	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17420101	0.84[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17479466	0.84[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17633463	0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2276648	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2276649	0.92[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2279105	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305935	0.91[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs3171927	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.90[ASN][1000 genomes]
rs3214058	0.84[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3214063	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3731930	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3731935	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731936	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4907231	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907232	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907307	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs4907308	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4907309	0.84[AMR][1000 genomes]
rs4907310	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4907311	0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4907312	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56027554	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56800261	0.85[AMR][1000 genomes]
rs57406815	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58328293	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59966106	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59979953	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153033	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62153034	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62153035	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62153039	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153041	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153898	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153900	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153901	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62153902	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153905	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153906	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153915	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62153923	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6737429	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6755877	0.82[AMR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7562544	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7562544	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs7562544	CIAO1	cis	lymphoblastoid	seeQTL
rs7562544	CIAO1	cis	Adipose Subcutaneous	GTEx
rs7562544	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs7562544	AC008268.2	cis	Artery Tibial	GTEx
rs7562544	AC008268.2	cis	lung	GTEx
rs7562544	AC008268.2	cis	Muscle Skeletal	GTEx
rs7562544	CIAO1	cis	Esophagus Mucosa	GTEx
rs7562544	CIAO1	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:97002000-97007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:97002000-97036000	Weak transcription	Gastric	stomach
4	chr2:97002200-97006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr2:97002200-97007200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:97002200-97008000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:97002200-97018800	Weak transcription	Right Atrium	heart
8	chr2:97002200-97037600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:97002400-97007200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:97002400-97007200	Weak transcription	Fetal Brain Female	brain
11	chr2:97002400-97007200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:97002400-97007400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:97002400-97007400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:97002400-97007400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:97002400-97007400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:97002400-97007600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:97002400-97012600	Weak transcription	Placenta	Placenta
18	chr2:97002400-97016200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:97002400-97018800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:97002600-97007000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:97002600-97007200	Weak transcription	Fetal Stomach	stomach
22	chr2:97002600-97007400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:97002600-97007600	Weak transcription	HSMM	muscle
24	chr2:97002600-97009800	Weak transcription	Fetal Kidney	kidney
25	chr2:97002600-97011800	Weak transcription	Small Intestine	intestine
26	chr2:97002600-97017400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:97002600-97031600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:97002800-97006800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:97002800-97006800	Weak transcription	NHLF	lung
30	chr2:97002800-97007000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:97002800-97007200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:97002800-97007200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:97002800-97007200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:97002800-97007400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:97002800-97007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr2:97002800-97007400	Weak transcription	Fetal Intestine Large	intestine
37	chr2:97002800-97007600	Weak transcription	Fetal Lung	lung
38	chr2:97002800-97007600	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:97002800-97007800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:97002800-97009800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:97002800-97010400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:97002800-97015400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:97002800-97018800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:97002800-97040000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:97003000-97006800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:97003000-97007200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:97003000-97007200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:97003000-97007400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:97003000-97007400	Weak transcription	Brain Germinal Matrix	brain
50	chr2:97003000-97007400	Weak transcription	Fetal Intestine Small	intestine

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