Variant report

Variant	rs62153902
Chromosome Location	chr2:96987742-96987743
allele	A/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	POLR2A	chr2:96987250-96987774	U87	brain:	n/a	n/a
2	EBF1	chr2:96986983-96988023	GM12878	blood:	n/a	chr2:96987466-96987477
3	E2F6	chr2:96986729-96988145	H1-hESC	embryonic stem cell:	n/a	chr2:96987699-96987708 chr2:96987673-96987680
4	PAX5	chr2:96987627-96987908	GM12892	blood:	n/a	chr2:96987783-96987802
5	MAZ	chr2:96986874-96987975	K562	blood:	n/a	n/a
6	BCLAF1	chr2:96987304-96988061	GM12878	blood:	n/a	chr2:96987490-96987503
7	ELF1	chr2:96986845-96987953	GM12878	blood:	n/a	n/a
8	UBTF	chr2:96986774-96988049	K562	blood:	n/a	n/a
9	TCF7L2	chr2:96986669-96988087	HCT-116	colon:	n/a	chr2:96988031-96988038
10	POLR2A	chr2:96987639-96987932	HCT-116	colon:	n/a	n/a
11	STAT1	chr2:96986914-96987995	GM12878	blood:	n/a	n/a
12	E2F6	chr2:96986769-96988111	H1-hESC	embryonic stem cell:	n/a	chr2:96987699-96987708 chr2:96987673-96987680
13	ATF2	chr2:96987417-96988137	GM12878	blood:	n/a	n/a
14	YY1	chr2:96987437-96987855	K562	blood:	n/a	n/a
15	YY1	chr2:96987399-96987958	GM12892	blood:	n/a	n/a
16	POLR2A	chr2:96987018-96987969	GM10847	blood:	n/a	n/a
17	CTCF	chr2:96987700-96987850	GM12872	blood:	n/a	n/a
18	POLR2A	chr2:96986860-96987937	PFSK-1	brain:	n/a	n/a
19	MAX	chr2:96986767-96988097	HepG2	liver:	n/a	n/a
20	YY1	chr2:96987613-96987836	K562	blood:	n/a	n/a
21	PAX5	chr2:96987562-96987993	GM12891	blood:	n/a	chr2:96987783-96987802
22	CTCF	chr2:96987740-96987890	HUVEC	blood vessel:	n/a	n/a
23	MAZ	chr2:96987430-96987790	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:96987373-96987933	GM12878	blood:	n/a	n/a
25	SIN3A	chr2:96986730-96987987	H1-hESC	embryonic stem cell:	n/a	n/a
26	ELK1	chr2:96987441-96988030	GM12878	blood:	n/a	n/a
27	RELA	chr2:96986571-96988062	GM19099	blood:	n/a	n/a
28	POLR2A	chr2:96986854-96987961	GM12878	blood:	n/a	n/a
29	SP1	chr2:96987485-96988063	A549	lung:	n/a	chr2:96987768-96987782 chr2:96987699-96987709 chr2:96987698-96987710 chr2:96987699-96987708 chr2:96987700-96987709
30	MAX	chr2:96986844-96987999	K562	blood:	n/a	n/a
31	MAX	chr2:96986615-96988161	K562	blood:	n/a	n/a
32	MTA3	chr2:96987315-96988107	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:96986740-96987997	GM18505	blood:	n/a	n/a
34	CHD2	chr2:96986858-96987998	GM12878	blood:	n/a	chr2:96987673-96987680
35	PAX5	chr2:96987465-96987989	GM12878	blood:	n/a	chr2:96987783-96987802
36	CTCF	chr2:96987700-96987850	GM12869	blood:	n/a	n/a
37	SIN3AK20	chr2:96987357-96987857	SK-N-SH	brain:	n/a	n/a
38	CHD2	chr2:96986819-96988059	H1-hESC	embryonic stem cell:	n/a	chr2:96987673-96987680
39	MYC	chr2:96986757-96987990	H1-hESC	embryonic stem cell:	n/a	n/a
40	RUNX3	chr2:96986454-96988081	GM12878	blood:	n/a	n/a
41	FOXA1	chr2:96987705-96988044	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:96986604-96988037	GM12878	blood:	n/a	n/a
43	ZNF143	chr2:96986938-96988003	H1-hESC	embryonic stem cell:	n/a	n/a
44	E2F6	chr2:96986755-96988090	K562	blood:	n/a	chr2:96987699-96987708 chr2:96987673-96987680
45	CTCF	chr2:96987720-96987870	NHDF-neo	bronchial:	n/a	n/a
46	SMC3	chr2:96987467-96988009	Hela-S3	cervix:	n/a	chr2:96987725-96987735 chr2:96987634-96987644
47	POLR2A	chr2:96986808-96987990	GM12892	blood:	n/a	n/a
48	EP300	chr2:96987481-96988017	GM12878	blood:	n/a	chr2:96987935-96987945 chr2:96987519-96987532
49	EGR1	chr2:96987537-96987897	GM12878	blood:	n/a	chr2:96987695-96987709 chr2:96987661-96987671 chr2:96987694-96987707 chr2:96987706-96987719 chr2:96987660-96987674
50	JUND	chr2:96986799-96987975	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:96987704-96987754	LNCaP	prostate:	n/a
2	chr2:96987726-96987776	ECC-1	luminal epithelium:	n/a
3	chr2:96987704-96987754	AG04449	skin:	fetal
4	chr2:96987704-96987754	BJ	skin:	n/a
5	chr2:96987704-96987754	HUVEC	blood vessel:	n/a
6	chr2:96987704-96987754	PrEC	prostate:	n/a
7	chr2:96987704-96987754	H1-hESC	embryonic stem cell:	embryo
8	chr2:96987726-96987776	GM12891	blood:	n/a
9	chr2:96987726-96987776	AG10803	skin:	n/a
10	chr2:96987704-96987754	MCF-7	breast:	n/a
11	chr2:96987726-96987776	HAEpiC	amniotic membrane:	n/a
12	chr2:96987704-96987754	A549	lung:	n/a
13	chr2:96987704-96987754	AG09319	gingival:	n/a
14	chr2:96987704-96987754	HNPCEpiC	eye:	n/a
15	chr2:96987704-96987754	GM19239	blood:	n/a
16	chr2:96987726-96987776	HCPEpiC	choroid plexus:	n/a
17	chr2:96987704-96987754	GM06990	blood:	n/a
18	chr2:96987726-96987776	A549	lung:	n/a
19	chr2:96987726-96987776	SK-N-SH_RA	brain:	n/a
20	chr2:96987704-96987754	BE2_C	brain:	n/a
21	chr2:96987704-96987754	SAEC	small airway:	n/a
22	chr2:96987726-96987776	AG04450	lung:	fetal
23	chr2:96987704-96987754	SK-N-SH_RA	brain:	n/a
24	chr2:96987704-96987754	SKMC	muscle:	n/a
25	chr2:96987704-96987754	AG09309	skin:	n/a
26	chr2:96987704-96987754	NH-A	brain:	n/a
27	chr2:96987726-96987776	SK-N-SH	brain:	n/a
28	chr2:96987726-96987776	H1-hESC	embryonic stem cell:	embryo
29	chr2:96987704-96987754	HL-60	blood:	n/a
30	chr2:96987726-96987776	HCT-116	colon:	n/a
31	chr2:96987704-96987754	SK-N-SH	brain:	n/a
32	chr2:96987704-96987754	HMEC	breast:	n/a
33	chr2:96987726-96987776	CMK	blood:	n/a
34	chr2:96987704-96987754	HepG2	liver:	n/a
35	chr2:96987726-96987776	AG09319	gingival:	n/a
36	chr2:96987726-96987776	IMR90	lung:	fetal
37	chr2:96987726-96987776	HRE	kidney:	n/a
38	chr2:96987726-96987776	GM19239	blood:	n/a
39	chr2:96987704-96987754	HIPEpiC	eye:	n/a
40	chr2:96987726-96987776	SAEC	small airway:	n/a
41	chr2:96987704-96987754	U87	brain:	n/a
42	chr2:96987726-96987776	AoSMC	blood vessel:	n/a
43	chr2:96987704-96987754	AG04450	lung:	fetal
44	chr2:96987726-96987776	Jurkat	blood:	n/a
45	chr2:96987726-96987776	HCM	heart:	n/a
46	chr2:96987726-96987776	PANC-1	pancreas:	n/a
47	chr2:96987726-96987776	HepG2	liver:	n/a
48	chr2:96987704-96987754	HEEpiC	esophagus:	n/a
49	chr2:96987726-96987776	GM12878	blood:	n/a
50	chr2:96987704-96987754	GM12878	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96985829..96988106-chr2:96989038..96991454,2	MCF-7	breast:
2	chr2:96968224..96973301-chr2:96983171..96988936,6	MCF-7	breast:
3	chr2:96969674..96973937-chr2:96983543..96988332,6	MCF-7	breast:
4	chr2:96954818..96956480-chr2:96987207..96989658,2	K562	blood:

Variant related genes	Relation type
ENSG00000230747	TF binding region
ITPRIPL1	TF binding region
ITPRIPL1	CpG island
ENSG00000230747	CpG island
ENSG00000144028	Chromatin interaction
ENSG00000198885	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1044594	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1048675	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11903461	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17420101	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17479466	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17633463	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2276648	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2276649	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2279105	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3171927	0.99[ASN][1000 genomes]
rs3214058	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3214063	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3731930	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3731935	0.81[EUR][1000 genomes]
rs3731936	0.81[EUR][1000 genomes]
rs4907231	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907232	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4907307	0.83[AMR][1000 genomes]
rs4907308	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4907309	0.84[AMR][1000 genomes]
rs4907310	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4907311	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4907312	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56027554	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56800261	0.85[AMR][1000 genomes];0.82[EUR][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];0.92[EUR][1000 genomes]
rs59979953	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62153033	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153034	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153035	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62153039	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153041	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153898	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153900	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153901	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62153905	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153906	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153915	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62153923	0.81[AMR][1000 genomes]
rs6755877	0.82[AMR][1000 genomes]
rs7562544	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62153902	AC008268.2	cis	Artery Tibial	GTEx
rs62153902	CIAO1	cis	Esophagus Mucosa	GTEx
rs62153902	AC008268.2	cis	lung	GTEx
rs62153902	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs62153902	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs62153902	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs62153902	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs62153902	CIAO1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96984600-96988200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:96986000-96987800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:96986000-96988600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:96986200-96988200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr2:96986200-96988200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr2:96986400-96988200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:96986400-96988200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr2:96986400-96988200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr2:96986400-96988200	Flanking Bivalent TSS/Enh	Dnd41	blood
10	chr2:96986600-96987800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:96986600-96987800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:96986600-96987800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:96986600-96987800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
14	chr2:96986600-96988000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:96986600-96988000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:96986600-96988000	Flanking Active TSS	Liver	Liver
17	chr2:96986600-96988000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:96986600-96988000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr2:96986600-96988000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
20	chr2:96986600-96988000	Active TSS	Right Atrium	heart
21	chr2:96986600-96988000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr2:96986600-96988000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
23	chr2:96986600-96988000	Flanking Bivalent TSS/Enh	NHEK	skin
24	chr2:96986600-96988200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr2:96986600-96988200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:96986600-96988200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr2:96986600-96988200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
28	chr2:96986600-96988200	Active TSS	Thymus	Thymus
29	chr2:96986600-96988200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr2:96986800-96987800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:96986800-96987800	Bivalent Enhancer	Fetal Brain Male	brain
32	chr2:96986800-96987800	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr2:96986800-96987800	Active TSS	GM12878-XiMat	blood
34	chr2:96986800-96987800	Active TSS	HSMMtube	muscle
35	chr2:96986800-96987800	Active TSS	NHLF	lung
36	chr2:96986800-96988000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr2:96986800-96988000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:96986800-96988000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
39	chr2:96986800-96988000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
40	chr2:96986800-96988000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:96986800-96988000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:96986800-96988000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:96986800-96988000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr2:96986800-96988000	Bivalent/Poised TSS	Fetal Kidney	kidney
45	chr2:96986800-96988000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
46	chr2:96986800-96988000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr2:96986800-96988000	Flanking Active TSS	Placenta	Placenta
48	chr2:96986800-96988000	Flanking Bivalent TSS/Enh	HepG2	liver
49	chr2:96986800-96988000	Flanking Active TSS	HMEC	breast
50	chr2:96986800-96988200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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