Variant report

Variant	rs1060906
Chromosome Location	chr2:114735416-114735417
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	CTCF	chr2:114735340-114735490	HBMEC	blood vessel:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
2	MAFK	chr2:114735172-114736138	HepG2	liver:	n/a	chr2:114735694-114735704
3	CTCF	chr2:114735400-114735550	HRPEpiC	eye:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
4	RAD21	chr2:114735272-114735803	HCT-116	colon:	n/a	chr2:114735462-114735481 chr2:114735679-114735692
5	CTCF	chr2:114735360-114735510	AG04449	skin:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
6	CEBPZ	chr2:114735098-114736250	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:114734609-114736884	HepG2	liver:	n/a	n/a
8	YY1	chr2:114735356-114736098	HepG2	liver:	n/a	n/a
9	MYBL2	chr2:114734478-114738477	HepG2	liver:	n/a	n/a
10	CTCF	chr2:114735334-114735509	MCF-7	breast:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
11	POLR2A	chr2:114734525-114735486	GM12891	blood:	n/a	n/a
12	POLR2A	chr2:114734945-114735653	U87	brain:	n/a	n/a
13	CTCF	chr2:114735340-114735490	HCM	heart:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
14	CEBPB	chr2:114735042-114736758	HepG2	liver:	n/a	chr2:114735799-114735810
15	CTCF	chr2:114735340-114735490	SAEC	small airway:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
16	TEAD4	chr2:114734792-114736870	HepG2	liver:	n/a	n/a
17	SP1	chr2:114734856-114736305	HepG2	liver:	n/a	n/a
18	CTCF	chr2:114735289-114735629	H1-hESC	embryonic stem cell:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
19	FOXA2	chr2:114734545-114736465	HepG2	liver:	n/a	n/a
20	CEBPB	chr2:114735263-114735486	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:114734568-114736048	PANC-1	pancreas:	n/a	n/a
22	CTCF	chr2:114735400-114735550	HCFaa	heart:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
23	CTCF	chr2:114735322-114735566	MCF-7	breast:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
24	CTCF	chr2:114735360-114735510	SK-N-SH_RA	brain:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
25	RAD21	chr2:114735252-114735668	IMR90	lung:	n/a	chr2:114735462-114735481
26	CTCF	chr2:114735376-114735540	Lung_OC	lung:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
27	JUND	chr2:114735094-114735492	HepG2	liver:	n/a	n/a
28	CTCF	chr2:114735340-114735490	HRE	kidney:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
29	CHD2	chr2:114734698-114736606	HepG2	liver:	n/a	n/a
30	RAD21	chr2:114735175-114735828	MCF-7	breast:	n/a	chr2:114735462-114735481 chr2:114735679-114735692
31	HNF4A	chr2:114735100-114736122	HepG2	liver:	n/a	chr2:114735661-114735669 chr2:114735435-114735443
32	MAX	chr2:114735335-114736267	HCT-116	colon:	n/a	chr2:114735696-114735705 chr2:114735695-114735704
33	FOSL2	chr2:114734637-114736836	HepG2	liver:	n/a	chr2:114735695-114735704 chr2:114735694-114735706 chr2:114735697-114735704 chr2:114735971-114735982 chr2:114735696-114735704
34	POLR2A	chr2:114734270-114737182	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:114734593-114736611	HepG2	liver:	n/a	n/a
36	CREB1	chr2:114734601-114737261	HepG2	liver:	n/a	n/a
37	HEY1	chr2:114734625-114737653	HepG2	liver:	n/a	n/a
38	SMC3	chr2:114735356-114735611	Hela-S3	cervix:	n/a	chr2:114735463-114735477
39	FOSL2	chr2:114734993-114736280	HepG2	liver:	n/a	chr2:114735695-114735704 chr2:114735694-114735706 chr2:114735697-114735704 chr2:114735971-114735982 chr2:114735696-114735704
40	CTCF	chr2:114735360-114735510	HCM	heart:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
41	MYBL2	chr2:114734556-114736571	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:114734646-114736832	HepG2	liver:	n/a	n/a
43	FOXA1	chr2:114734947-114736371	HepG2	liver:	n/a	n/a
44	CTCF	chr2:114735232-114735777	HepG2	liver:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
45	CTCF	chr2:114735403-114735467	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr2:114735260-114735695	ECC-1	luminal epithelium:	n/a	chr2:114735462-114735481 chr2:114735679-114735692
47	CTCF	chr2:114735380-114735530	HRE	kidney:	n/a	chr2:114735461-114735479 chr2:114735463-114735484
48	POLR2A	chr2:114734601-114735498	HepG2	liver:	n/a	n/a
49	POLR2A	chr2:114734635-114736299	A549	lung:	n/a	n/a
50	POLR2A	chr2:114734584-114735590	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:114727885..114731158-chr2:114732543..114736928,5	K562	blood:
2	chr2:114735108..114735885-chr2:115840904..115841609,2	MCF-7	breast:
3	chr2:114735300..114736037-chr2:115300297..115300842,2	MCF-7	breast:
4	chr2:114735006..114735845-chr2:115308620..115309837,4	MCF-7	breast:
5	chr2:114735044..114736090-chr2:115308641..115309989,10	MCF-7	breast:
6	chr2:114734985..114735963-chr2:115300641..115301514,3	MCF-7	breast:
7	chr2:114648039..114650130-chr2:114735368..114736887,2	K562	blood:
8	chr2:114735196..114736318-chr2:114959110..114959760,3	MCF-7	breast:
9	chr2:114735119..114736107-chr2:115301018..115301565,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTR3-1	chr2:114735195-114737211	NONHSAT073855

Variant related genes	Relation type
ENSG00000234199	TF binding region
ENSG00000243179	TF binding region
ENSG00000115091	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10183875	1.00[CEU][hapmap];0.82[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10197726	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11123214	1.00[JPT][hapmap]
rs11685654	1.00[JPT][hapmap]
rs156703	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs156704	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs156705	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs156709	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs156710	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs156711	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs156712	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs156714	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17269836	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs275416	0.88[EUR][1000 genomes]
rs276317	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs276818	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs276820	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs276827	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs467954	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55701938	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55748015	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6542187	0.93[EUR][1000 genomes]
rs6705036	0.93[EUR][1000 genomes]
rs72837203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1060906	NPHP1	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114705200-114736000	Weak transcription	Gastric	stomach
2	chr2:114705200-114737600	Weak transcription	Esophagus	oesophagus
3	chr2:114710400-114735800	Weak transcription	Colonic Mucosa	Colon
4	chr2:114713800-114736200	Weak transcription	Fetal Stomach	stomach
5	chr2:114715000-114744000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:114715200-114735600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:114715600-114737000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:114718800-114743200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:114721200-114735800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:114727600-114735600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:114727600-114736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:114727600-114736800	Weak transcription	A549	lung
13	chr2:114729000-114735600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:114729600-114737000	Weak transcription	Placenta	Placenta
15	chr2:114732400-114737400	Weak transcription	Lung	lung
16	chr2:114732600-114735600	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:114733200-114736000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr2:114733400-114735600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:114733400-114737400	Weak transcription	GM12878-XiMat	blood
20	chr2:114733400-114741200	Weak transcription	Liver	Liver
21	chr2:114733400-114743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:114733800-114735800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:114733800-114736600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:114733800-114736800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:114733800-114741600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:114734000-114736200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr2:114734000-114736800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:114734000-114737200	Enhancers	HMEC	breast
29	chr2:114734000-114737800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:114734000-114738000	Enhancers	Pancreas	Pancrea
31	chr2:114734000-114746000	Weak transcription	Aorta	Aorta
32	chr2:114734000-114751800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:114734200-114736200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:114734200-114736800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:114734200-114737000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:114734200-114737800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:114734400-114735600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:114734400-114735600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:114734400-114736600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:114734400-114749800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:114734600-114735800	Flanking Active TSS	HepG2	liver
42	chr2:114734600-114736200	Enhancers	HSMM	muscle
43	chr2:114734600-114736200	Enhancers	HSMMtube	muscle
44	chr2:114734600-114736600	Enhancers	Fetal Intestine Large	intestine
45	chr2:114734600-114736600	Enhancers	NH-A	brain
46	chr2:114734600-114736800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:114734600-114738200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:114734800-114736000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:114734800-114736000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:114734800-114736000	Enhancers	NHEK	skin

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