Variant report

Variant	rs17366322
Chromosome Location	chr2:11272784-11272785
allele	G/T
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	CTCF	chr2:11272703-11273086	SK-N-SH_RA	brain:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
2	RAD21	chr2:11272585-11273337	HepG2	liver:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
3	GABPA	chr2:11272628-11273328	A549	lung:	n/a	n/a
4	NR3C1	chr2:11272714-11273622	A549	lung:	n/a	chr2:11273361-11273375 chr2:11273360-11273376 chr2:11273361-11273375 chr2:11273360-11273376 chr2:11273357-11273378 chr2:11273090-11273104 chr2:11273360-11273376 chr2:11273360-11273376 chr2:11273355-11273381 chr2:11273358-11273371
5	TCF12	chr2:11272715-11273346	A549	lung:	n/a	n/a
6	REST	chr2:11272590-11273463	A549	lung:	n/a	chr2:11273188-11273197
7	CEBPB	chr2:11272777-11273302	IMR90	lung:	n/a	n/a
8	ELF1	chr2:11272608-11273291	K562	blood:	n/a	n/a
9	SMC3	chr2:11272685-11273402	HepG2	liver:	n/a	chr2:11272906-11272920
10	MAZ	chr2:11272719-11273271	Hela-S3	cervix:	n/a	n/a
11	RCOR1	chr2:11272629-11273221	K562	blood:	n/a	n/a
12	SMC3	chr2:11272698-11273286	GM12878	blood:	n/a	chr2:11272906-11272920
13	MAX	chr2:11272471-11273510	MCF-7	breast:	n/a	n/a
14	ELK1	chr2:11272764-11273207	GM12878	blood:	n/a	n/a
15	CTCF	chr2:11272712-11273102	ECC-1	luminal epithelium:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
16	RAD21	chr2:11272690-11273135	Hela-S3	cervix:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
17	GTF2F1	chr2:11272685-11273086	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr2:11272743-11273039	MCF-7	breast:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
19	SP4	chr2:11272686-11273354	H1-hESC	embryonic stem cell:	n/a	chr2:11273008-11273024 chr2:11273067-11273083 chr2:11273170-11273186 chr2:11273014-11273025
20	CTCF	chr2:11272654-11273103	H1-hESC	embryonic stem cell:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
21	REST	chr2:11272683-11273399	PFSK-1	brain:	n/a	chr2:11273188-11273197
22	RCOR1	chr2:11272664-11273198	Hela-S3	cervix:	n/a	n/a
23	TBP	chr2:11272689-11273439	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr2:11272764-11273045	Medullo	brain:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
25	MYC	chr2:11272781-11273265	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr2:11272659-11273257	A549	lung:	n/a	n/a
27	EBF1	chr2:11272685-11273055	GM12878	blood:	n/a	n/a
28	SIN3AK20	chr2:11272763-11273399	HepG2	liver:	n/a	n/a
29	CTCF	chr2:11272749-11273045	GM10248	blood:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
30	ZNF143	chr2:11272716-11273165	GM12878	blood:	n/a	n/a
31	CTCF	chr2:11272677-11273113	H1-hESC	embryonic stem cell:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
32	MXI1	chr2:11272770-11273358	H1-hESC	embryonic stem cell:	n/a	chr2:11273196-11273211
33	MAX	chr2:11272720-11273296	A549	lung:	n/a	n/a
34	YY1	chr2:11272744-11273088	K562	blood:	n/a	n/a
35	CTCF	chr2:11272780-11273032	T-47D	breast:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
36	ZKSCAN1	chr2:11272774-11273282	Hela-S3	cervix:	n/a	n/a
37	ELF1	chr2:11272615-11273369	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:11272784-11272840	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr2:11272529-11273226	A549	lung:	n/a	chr2:11272908-11272921 chr2:11272905-11272924
40	IRF1	chr2:11272743-11273283	K562	blood:	n/a	chr2:11273236-11273250 chr2:11273237-11273248 chr2:11273236-11273249 chr2:11273236-11273250 chr2:11273238-11273249
41	CTCF	chr2:11272753-11273081	A549	lung:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
42	SMC3	chr2:11272659-11273459	Hela-S3	cervix:	n/a	chr2:11272906-11272920
43	RFX5	chr2:11272757-11273292	Hela-S3	cervix:	n/a	chr2:11273197-11273212
44	TCF12	chr2:11272592-11273269	ECC-1	luminal epithelium:	n/a	n/a
45	E2F4	chr2:11272753-11273261	GM12878	blood:	n/a	n/a
46	CTCF	chr2:11272780-11272930	NHLF	lung:	n/a	chr2:11272907-11272920 chr2:11272904-11272922 chr2:11272906-11272927
47	MAX	chr2:11272779-11273187	GM12878	blood:	n/a	n/a
48	MYC	chr2:11272736-11273179	K562	blood:	n/a	n/a
49	USF2	chr2:11272686-11272910	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr2:11272760-11272910	MCF-7	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:11272783-11272833	HMEC	breast:	n/a
2	chr2:11272783-11272833	SK-N-SH_RA	brain:	n/a
3	chr2:11272783-11272833	AG09319	gingival:	n/a
4	chr2:11272783-11272833	LNCaP	prostate:	n/a
5	chr2:11272783-11272833	ProgFib	skin:	n/a
6	chr2:11272783-11272833	ECC-1	luminal epithelium:	n/a
7	chr2:11272783-11272833	SKMC	muscle:	n/a
8	chr2:11272783-11272833	HCF	heart:	n/a
9	chr2:11272783-11272833	NHDF-neo	bronchial:	n/a
10	chr2:11272783-11272833	HCT-116	colon:	n/a
11	chr2:11272783-11272833	GM12878	blood:	n/a
12	chr2:11272783-11272833	HPAEpiC	pulmonary alveolar:	n/a
13	chr2:11272783-11272833	IMR90	lung:	fetal
14	chr2:11272783-11272833	HNPCEpiC	eye:	n/a
15	chr2:11272783-11272833	T-47D	breast:	n/a
16	chr2:11272783-11272833	Hepatocyte	liver:	n/a
17	chr2:11272783-11272833	K562	blood:	n/a
18	chr2:11272783-11272833	GM12892	blood:	n/a
19	chr2:11272783-11272833	Hela-S3	cervix:	n/a
20	chr2:11272783-11272833	AG10803	skin:	n/a
21	chr2:11272783-11272833	HAEpiC	amniotic membrane:	n/a
22	chr2:11272783-11272833	A549	lung:	n/a
23	chr2:11272783-11272833	NH-A	brain:	n/a
24	chr2:11272783-11272833	PrEC	prostate:	n/a
25	chr2:11272783-11272833	SAEC	small airway:	n/a
26	chr2:11272783-11272833	BJ	skin:	n/a
27	chr2:11272783-11272833	GM19239	blood:	n/a
28	chr2:11272783-11272833	AG09309	skin:	n/a
29	chr2:11272783-11272833	NHBE	bronchial:	n/a
30	chr2:11272783-11272833	AG04450	lung:	fetal
31	chr2:11272783-11272833	MCF10A-Er-Src	breast:	n/a
32	chr2:11272783-11272833	BE2_C	brain:	n/a
33	chr2:11272783-11272833	HL-60	blood:	n/a
34	chr2:11272783-11272833	H1-hESC	embryonic stem cell:	embryo
35	chr2:11272783-11272833	HCM	heart:	n/a
36	chr2:11272783-11272833	PFSK-1	brain:	n/a
37	chr2:11272783-11272833	SK-N-SH	brain:	n/a
38	chr2:11272783-11272833	HRCEpiC	kidney:	n/a
39	chr2:11272783-11272833	ovcar-3	ovarian:	n/a
40	chr2:11272783-11272833	HRPEpiC	eye:	n/a
41	chr2:11272783-11272833	RPTEC	kidney:	n/a
42	chr2:11272783-11272833	MCF-7	breast:	n/a
43	chr2:11272783-11272833	CMK	blood:	n/a
44	chr2:11272783-11272833	Caco-2	colon:	n/a
45	chr2:11272783-11272833	HEEpiC	esophagus:	n/a
46	chr2:11272783-11272833	HepG2	liver:	n/a
47	chr2:11272783-11272833	SK-N-MC	brain:	n/a
48	chr2:11272783-11272833	Jurkat	blood:	n/a
49	chr2:11272783-11272833	HCPEpiC	choroid plexus:	n/a
50	chr2:11272783-11272833	NT2-D1	testis:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11272046..11273363-chr2:11723821..11725006,6	K562	blood:
2	chr2:11272147..11274930-chr2:11671339..11675156,3	MCF-7	breast:
3	chr2:11271098..11275692-chr2:11293512..11297101,4	MCF-7	breast:
4	chr2:10828291..10832221-chr2:11269738..11273006,3	MCF-7	breast:
5	chr2:11269728..11273923-chr2:11678087..11684060,5	MCF-7	breast:
6	chr2:10971180..10977465-chr2:11267266..11272931,15	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ROCK2-3	chr2:11272399-11272896	ENSG00000145063
2	lnc-ROCK2-3	chr2:11272399-11272947	ENSG00000145063.10

Variant related genes	Relation type
ENSG00000145063	TF binding region
C2orf50	TF binding region
C2orf50	CpG island
ENSG00000145063	CpG island
ENSG00000143870	Chromatin interaction
ENSG00000243819	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000239899	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11676692	0.84[ASN][1000 genomes]
rs12470798	0.85[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12987119	0.82[ASN][1000 genomes]
rs12987956	1.00[YRI][hapmap]
rs13002429	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13021587	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1828930	0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2357993	0.87[ASN][1000 genomes]
rs2357994	0.87[ASN][1000 genomes]
rs36026430	0.84[ASN][1000 genomes]
rs55975936	0.84[ASN][1000 genomes]
rs727803	0.84[ASN][1000 genomes]
rs7581322	0.81[ASN][1000 genomes]
rs7586305	0.91[ASN][1000 genomes]
rs7606827	0.83[ASN][1000 genomes]
rs7608117	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17366322	IAH1	cis	cerebellum	SCAN
rs17366322	C2orf50	cis	parietal	SCAN
rs17366322	PQLC3	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11269800-11274000	Enhancers	Fetal Brain Male	brain
2	chr2:11270400-11272800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:11270400-11272800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:11270400-11273000	Weak transcription	Aorta	Aorta
5	chr2:11270400-11273000	Weak transcription	Esophagus	oesophagus
6	chr2:11270600-11272800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:11270600-11272800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:11270600-11272800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:11270600-11272800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:11270600-11272800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:11270600-11272800	Weak transcription	Ovary	ovary
12	chr2:11270600-11272800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:11270600-11272800	Weak transcription	Psoas Muscle	Psoas
14	chr2:11270600-11272800	Weak transcription	Right Atrium	heart
15	chr2:11270600-11272800	Weak transcription	Right Ventricle	heart
16	chr2:11270600-11272800	Weak transcription	HSMM	muscle
17	chr2:11270600-11273000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:11270600-11273000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:11270600-11273000	Weak transcription	Lung	lung
20	chr2:11270600-11273200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:11270800-11272800	Weak transcription	HMEC	breast
22	chr2:11270800-11273000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:11270800-11273000	Weak transcription	Fetal Heart	heart
24	chr2:11271000-11272800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:11271000-11273000	Weak transcription	Small Intestine	intestine
26	chr2:11271400-11273200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:11271400-11274200	Active TSS	Brain Anterior Caudate	brain
28	chr2:11271600-11272800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr2:11271800-11272800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:11271800-11273200	Active TSS	Brain Hippocampus Middle	brain
31	chr2:11271800-11273600	Active TSS	Brain Cingulate Gyrus	brain
32	chr2:11272200-11272800	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:11272200-11272800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:11272200-11272800	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr2:11272200-11273200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:11272400-11272800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:11272400-11272800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:11272400-11272800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:11272400-11272800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:11272400-11272800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:11272400-11272800	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr2:11272400-11272800	Enhancers	Colon Smooth Muscle	Colon
43	chr2:11272400-11272800	Enhancers	Fetal Intestine Large	intestine
44	chr2:11272400-11272800	Enhancers	Fetal Muscle Leg	muscle
45	chr2:11272400-11272800	Enhancers	Placenta	Placenta
46	chr2:11272400-11272800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
47	chr2:11272400-11272800	Bivalent Enhancer	Stomach Mucosa	stomach
48	chr2:11272400-11273000	Enhancers	NHLF	lung
49	chr2:11272400-11273400	Enhancers	Spleen	Spleen
50	chr2:11272400-11273600	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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