Variant report

Variant	rs2290368
Chromosome Location	chr2:152266473-152266474
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	FOXP2	chr2:152266140-152266690	PFSK-1	brain:	n/a	n/a
2	MYC	chr2:152266282-152266635	Hela-S3	cervix:	n/a	n/a
3	YY1	chr2:152266143-152267150	K562	blood:	n/a	chr2:152266416-152266428 chr2:152266577-152266586
4	POLR2A	chr2:152266182-152266788	GM12878	blood:	n/a	n/a
5	MYC	chr2:152266153-152266666	MCF10A-Er-Src	breast:	n/a	n/a
6	POU2F2	chr2:152266145-152266894	GM12891	blood:	n/a	n/a
7	EP300	chr2:152266114-152266586	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXA1	chr2:152266106-152266755	HepG2	liver:	n/a	chr2:152266453-152266468
9	EGR1	chr2:152266228-152266616	H1-hESC	embryonic stem cell:	n/a	chr2:152266510-152266524
10	STAT5A	chr2:152266200-152266553	GM12878	blood:	n/a	n/a
11	TBP	chr2:152265902-152267425	K562	blood:	n/a	n/a
12	YY1	chr2:152266039-152266852	H1-hESC	embryonic stem cell:	n/a	chr2:152266416-152266428 chr2:152266577-152266586
13	E2F6	chr2:152266172-152266863	A549	lung:	n/a	chr2:152266697-152266709 chr2:152266644-152266656 chr2:152266368-152266379
14	POLR2A	chr2:152266165-152267269	GM12878	blood:	n/a	n/a
15	TAF1	chr2:152266054-152267209	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr2:152266450-152266674	Lung_OC	lung:	n/a	chr2:152266607-152266623 chr2:152266608-152266621 chr2:152266606-152266624
17	POLR2A	chr2:152266126-152267497	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr2:152266146-152267291	H1-hESC	embryonic stem cell:	n/a	n/a
19	MYC	chr2:152266188-152267290	HepG2	liver:	n/a	chr2:152267051-152267060
20	CTCF	chr2:152266284-152266750	GM12891	blood:	n/a	chr2:152266607-152266623 chr2:152266608-152266621 chr2:152266606-152266624
21	SETDB1	chr2:152265988-152266598	U2OS	brain:	n/a	n/a
22	MYC	chr2:152265841-152267595	A549	lung:	n/a	chr2:152267051-152267060
23	TBL1XR1	chr2:152266075-152267048	K562	blood:	n/a	n/a
24	TCF12	chr2:152266118-152266649	A549	lung:	n/a	chr2:152266455-152266464
25	GABPA	chr2:152266172-152267262	K562	blood:	n/a	chr2:152267182-152267191
26	NFIC	chr2:152266064-152267200	HepG2	liver:	n/a	n/a
27	IRF3	chr2:152266195-152266546	GM12878	blood:	n/a	n/a
28	REST	chr2:152265952-152266729	A549	lung:	n/a	chr2:152266704-152266717
29	NFIC	chr2:152266020-152266776	GM12878	blood:	n/a	n/a
30	MAX	chr2:152266167-152267387	GM12878	blood:	n/a	chr2:152267051-152267060
31	SIN3AK20	chr2:152266166-152267376	HepG2	liver:	n/a	n/a
32	RAD21	chr2:152266049-152266788	H1-hESC	embryonic stem cell:	n/a	n/a
33	MAX	chr2:152266092-152267415	Hela-S3	cervix:	n/a	chr2:152267051-152267060
34	FOSL2	chr2:152265831-152266920	HepG2	liver:	n/a	chr2:152266852-152266863
35	ELF1	chr2:152266134-152267118	HepG2	liver:	n/a	n/a
36	E2F6	chr2:152265859-152267023	H1-hESC	embryonic stem cell:	n/a	chr2:152266697-152266709 chr2:152266644-152266656 chr2:152266368-152266379
37	SMC3	chr2:152266120-152266773	GM12878	blood:	n/a	chr2:152266608-152266622
38	EP300	chr2:152265981-152266669	K562	blood:	n/a	n/a
39	POLR2A	chr2:152266247-152267316	HUVEC	blood vessel:	n/a	n/a
40	RAD21	chr2:152266216-152266618	HepG2	liver:	n/a	n/a
41	ELK4	chr2:152266103-152267156	Hela-S3	cervix:	n/a	chr2:152266905-152266916
42	MAX	chr2:152265961-152267529	ECC-1	luminal epithelium:	n/a	chr2:152267051-152267060
43	YY1	chr2:152266084-152267172	GM12878	blood:	n/a	chr2:152266416-152266428 chr2:152266577-152266586
44	KAP1	chr2:152265982-152266615	U2OS	brain:	n/a	n/a
45	EGR1	chr2:152266203-152266749	GM12878	blood:	n/a	chr2:152266607-152266620 chr2:152266510-152266524 chr2:152266607-152266620
46	RAD21	chr2:152266138-152266814	SK-N-SH_RA	brain:	n/a	chr2:152266790-152266803
47	STAT3	chr2:152266116-152266588	MCF10A-Er-Src	breast:	n/a	n/a
48	MXI1	chr2:152265926-152267910	SK-N-SH	brain:	n/a	n/a
49	MYBL2	chr2:152265912-152267454	HepG2	liver:	n/a	n/a
50	USF1	chr2:152266004-152266753	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:152144813..152149803-chr2:152261382..152268379,11	K562	blood:
2	chr2:152262551..152270893-chr2:152273971..152280003,13	K562	blood:
3	chr2:152145011..152148288-chr2:152265460..152267609,4	MCF-7	breast:
4	chr2:152116678..152120470-chr2:152265032..152268454,8	MCF-7	breast:
5	chr2:152145849..152146532-chr2:152266419..152266964,2	MCF-7	breast:
6	chr2:152116022..152119511-chr2:152263980..152267786,5	K562	blood:
7	chr2:152146182..152146803-chr2:152266084..152266913,2	MCF-7	breast:
8	chr2:152116994..152118893-chr2:152266218..152268136,2	MCF-7	breast:
9	chr2:152144798..152147073-chr2:152265350..152268359,5	MCF-7	breast:

Variant related genes	Relation type
RIF1	TF binding region
ENSG00000080345	Chromatin interaction
ENSG00000123609	Chromatin interaction
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10173597	0.88[CEU][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10178027	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10197940	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10199519	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10204541	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10208356	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10210990	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680748	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11687344	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11693857	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13393021	0.86[CHB][hapmap]
rs13422366	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17806222	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs2290367	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444256	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs4500942	0.81[CEU][hapmap]
rs4664045	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4664423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6724796	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs6731486	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs67602292	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv834418	chr2:152205803-152385516	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290368	RIF1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152264800-152268000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:152265000-152268600	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:152265400-152267800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr2:152265600-152268200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr2:152265800-152267400	Active TSS	Stomach Smooth Muscle	stomach
6	chr2:152265800-152267600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr2:152266000-152266600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:152266000-152266600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:152266000-152266600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:152266000-152266800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:152266000-152266800	Active TSS	Fetal Brain Female	brain
12	chr2:152266000-152267000	Active TSS	Primary B cells from cord blood	blood
13	chr2:152266000-152267000	Active TSS	Adipose Nuclei	Adipose
14	chr2:152266000-152267200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:152266000-152267200	Active TSS	Primary T cells from cord blood	blood
16	chr2:152266000-152267200	Active TSS	Primary hematopoietic stem cells	blood
17	chr2:152266000-152267200	Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr2:152266000-152267200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:152266000-152267200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:152266000-152267200	Active TSS	Liver	Liver
21	chr2:152266000-152267200	Active TSS	Osteobl	bone
22	chr2:152266000-152267400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:152266000-152267400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:152266000-152267400	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr2:152266000-152267400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:152266000-152267400	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr2:152266000-152267400	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr2:152266000-152267400	Active TSS	Brain Anterior Caudate	brain
29	chr2:152266000-152267400	Active TSS	Brain Hippocampus Middle	brain
30	chr2:152266000-152267400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:152266000-152267400	Active TSS	Brain Substantia Nigra	brain
32	chr2:152266000-152267400	Active TSS	Duodenum Mucosa	Duodenum
33	chr2:152266000-152267400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr2:152266000-152267400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr2:152266000-152267400	Active TSS	Fetal Heart	heart
36	chr2:152266000-152267400	Active TSS	Rectal Smooth Muscle	rectum
37	chr2:152266000-152267400	Active TSS	HUVEC	blood vessel
38	chr2:152266000-152267600	Active TSS	Brain Cingulate Gyrus	brain
39	chr2:152266000-152267600	Active TSS	Colonic Mucosa	Colon
40	chr2:152266000-152267600	Active TSS	Fetal Intestine Small	intestine
41	chr2:152266000-152267600	Active TSS	Fetal Lung	lung
42	chr2:152266000-152267600	Active TSS	Psoas Muscle	Psoas
43	chr2:152266000-152267600	Active TSS	Right Ventricle	heart
44	chr2:152266000-152267600	Active TSS	Thymus	Thymus
45	chr2:152266000-152267600	Active TSS	HSMMtube	muscle
46	chr2:152266000-152267600	Active TSS	NHEK	skin
47	chr2:152266000-152267800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:152266000-152267800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:152266000-152267800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:152266000-152267800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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