Variant report

Variant	rs2241842
Chromosome Location	chr2:111879415-111879416
allele	C/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	MAX	chr2:111877563-111881015	NB4	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
2	E2F6	chr2:111876311-111880584	H1-hESC	embryonic stem cell:	n/a	chr2:111876443-111876455 chr2:111878414-111878423 chr2:111880549-111880558 chr2:111880095-111880104 chr2:111877747-111877759 chr2:111877347-111877357 chr2:111876622-111876632 chr2:111877478-111877490 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111880318-111880330 chr2:111878285-111878294 chr2:111878171-111878181 chr2:111880053-111880060
3	TCF12	chr2:111877680-111880212	A549	lung:	n/a	n/a
4	SIN3AK20	chr2:111877611-111881217	MCF-7	breast:	n/a	n/a
5	CHD1	chr2:111878621-111881270	H1-hESC	embryonic stem cell:	n/a	chr2:111878901-111878911
6	CHD2	chr2:111879396-111880350	GM12878	blood:	n/a	n/a
7	MAX	chr2:111879364-111879516	K562	blood:	n/a	n/a
8	MTA3	chr2:111878588-111879518	GM12878	blood:	n/a	n/a
9	TCF12	chr2:111877517-111879634	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr2:111879163-111880376	GM12892	blood:	n/a	n/a
11	POLR2A	chr2:111877806-111880414	GM12878	blood:	n/a	n/a
12	HCFC1	chr2:111877979-111880854	K562	blood:	n/a	n/a
13	POLR2A	chr2:111877942-111881067	IMR90	lung:	n/a	n/a
14	TCF3	chr2:111879342-111879622	GM12878	blood:	n/a	n/a
15	E2F6	chr2:111878578-111880256	A549	lung:	n/a	chr2:111880095-111880104 chr2:111878679-111878691 chr2:111880053-111880060
16	MAX	chr2:111877542-111881163	HepG2	liver:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
17	POLR2A	chr2:111877432-111881054	K562	blood:	n/a	n/a
18	RUNX3	chr2:111879101-111879426	GM12878	blood:	n/a	n/a
19	SMARCB1	chr2:111877080-111881031	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:111877652-111881216	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr2:111877906-111880742	K562	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
22	ZKSCAN1	chr2:111878027-111879455	Hela-S3	cervix:	n/a	n/a
23	RCOR1	chr2:111879101-111881089	K562	blood:	n/a	n/a
24	E2F6	chr2:111877723-111880882	Hela-S3	cervix:	n/a	chr2:111878414-111878423 chr2:111880549-111880558 chr2:111880095-111880104 chr2:111877747-111877759 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111880318-111880330 chr2:111878285-111878294 chr2:111878171-111878181 chr2:111880053-111880060
25	POLR2A	chr2:111877744-111880423	NB4	blood:	n/a	n/a
26	MYC	chr2:111877505-111879474	K562	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
27	SIN3AK20	chr2:111879305-111879535	A549	lung:	n/a	n/a
28	MAZ	chr2:111877230-111879730	GM12878	blood:	n/a	chr2:111878235-111878244 chr2:111878683-111878693 chr2:111877479-111877489 chr2:111879218-111879227
29	UBTF	chr2:111877688-111881146	K562	blood:	n/a	n/a
30	MXI1	chr2:111877406-111881885	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr2:111879402-111880124	GM12878	blood:	n/a	n/a
32	BHLHE40	chr2:111877526-111880906	K562	blood:	n/a	chr2:111878164-111878180 chr2:111878158-111878174 chr2:111879083-111879099 chr2:111878389-111878405 chr2:111880077-111880093 chr2:111878166-111878182 chr2:111879143-111879159
33	SIN3AK20	chr2:111877950-111881096	PANC-1	pancreas:	n/a	n/a
34	CTBP2	chr2:111874524-111881050	H1-hESC	embryonic stem cell:	n/a	n/a
35	TCF12	chr2:111878544-111879427	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr2:111877766-111881072	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr2:111877690-111879624	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr2:111877803-111881080	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr2:111879265-111880311	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAZ	chr2:111879285-111881309	IMR90	lung:	n/a	n/a
41	MAX	chr2:111877586-111880464	A549	lung:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
42	POLR2A	chr2:111878174-111880226	GM12878	blood:	n/a	n/a
43	MAX	chr2:111877544-111881099	MCF-7	breast:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
44	POLR2A	chr2:111877091-111880269	Raji	blood:	n/a	n/a
45	CHD1	chr2:111877818-111879923	GM12878	blood:	n/a	chr2:111878005-111878015 chr2:111878901-111878911
46	POLR2A	chr2:111877827-111881856	HUVEC	blood vessel:	n/a	n/a
47	TAL1	chr2:111878930-111880129	K562	blood:	n/a	n/a
48	POLR2A	chr2:111879169-111880867	K562	blood:	n/a	n/a
49	ZNF263	chr2:111877354-111881804	HEK293-T-REx	kidney:	n/a	chr2:111877488-111877497
50	MAX	chr2:111877194-111879416	H1-hESC	embryonic stem cell:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111877479-111877489 chr2:111879218-111879227

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:111879378-111879428	HRPEpiC	eye:	n/a
2	chr2:111879378-111879428	LNCaP	prostate:	n/a
3	chr2:111879378-111879428	HUVEC	blood vessel:	n/a
4	chr2:111879378-111879428	HNPCEpiC	eye:	n/a
5	chr2:111879378-111879428	Jurkat	blood:	n/a
6	chr2:111879378-111879428	HEK293	kidney:	embryo
7	chr2:111879378-111879428	NHBE	bronchial:	n/a
8	chr2:111879378-111879428	HPAEpiC	pulmonary alveolar:	n/a
9	chr2:111879378-111879428	SK-N-SH_RA	brain:	n/a
10	chr2:111879378-111879428	ProgFib	skin:	n/a
11	chr2:111879378-111879428	PrEC	prostate:	n/a
12	chr2:111879378-111879428	HCT-116	colon:	n/a
13	chr2:111879378-111879428	HRCEpiC	kidney:	n/a
14	chr2:111879378-111879428	SK-N-MC	brain:	n/a
15	chr2:111879378-111879428	Hepatocyte	liver:	n/a
16	chr2:111879378-111879428	CMK	blood:	n/a
17	chr2:111879378-111879428	A549	lung:	n/a
18	chr2:111879378-111879428	AG04450	lung:	fetal
19	chr2:111879378-111879428	RPTEC	kidney:	n/a
20	chr2:111879378-111879428	AG09319	gingival:	n/a
21	chr2:111879378-111879428	PANC-1	pancreas:	n/a
22	chr2:111879378-111879428	T-47D	breast:	n/a
23	chr2:111879378-111879428	GM12878	blood:	n/a
24	chr2:111879378-111879428	SAEC	small airway:	n/a
25	chr2:111879378-111879428	H1-hESC	embryonic stem cell:	embryo
26	chr2:111879378-111879428	HL-60	blood:	n/a
27	chr2:111879378-111879428	BJ	skin:	n/a
28	chr2:111879378-111879428	HIPEpiC	eye:	n/a
29	chr2:111879378-111879428	HEEpiC	esophagus:	n/a
30	chr2:111879378-111879428	HCM	heart:	n/a
31	chr2:111879378-111879428	AG10803	skin:	n/a
32	chr2:111879378-111879428	SKMC	muscle:	n/a
33	chr2:111879378-111879428	HCF	heart:	n/a
34	chr2:111879378-111879428	SK-N-SH	brain:	n/a
35	chr2:111879378-111879428	AG09309	skin:	n/a
36	chr2:111879378-111879428	GM19239	blood:	n/a
37	chr2:111879378-111879428	K562	blood:	n/a
38	chr2:111879378-111879428	ovcar-3	ovarian:	n/a
39	chr2:111879378-111879428	GM12892	blood:	n/a
40	chr2:111879378-111879428	MCF-7	breast:	n/a
41	chr2:111879378-111879428	HCPEpiC	choroid plexus:	n/a
42	chr2:111879378-111879428	AG04449	skin:	fetal
43	chr2:111879378-111879428	MCF10A-Er-Src	breast:	n/a
44	chr2:111879378-111879428	ECC-1	luminal epithelium:	n/a
45	chr2:111879378-111879428	HepG2	liver:	n/a
46	chr2:111879378-111879428	HAEpiC	amniotic membrane:	n/a
47	chr2:111879378-111879428	NH-A	brain:	n/a
48	chr2:111879378-111879428	IMR90	lung:	fetal
49	chr2:111879378-111879428	Hela-S3	cervix:	n/a
50	chr2:111879378-111879428	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:111869458..111872537-chr2:111876483..111880583,5	MCF-7	breast:
2	chr2:111877393..111879713-chr2:112235053..112237981,2	K562	blood:
3	chr2:111434111..111436826-chr2:111878321..111880919,2	K562	blood:

Variant related genes	Relation type
BCL2L11	TF binding region
BCL2L11	CpG island
ENSG00000204581	Chromatin interaction
ENSG00000172965	Chromatin interaction
ENSG00000169679	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10166773	0.86[JPT][hapmap]
rs10189015	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10211562	0.84[ASN][1000 genomes]
rs1054873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11674517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13398360	0.86[JPT][hapmap]
rs1439287	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1821968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1837366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837368	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1877331	0.80[CHB][hapmap]
rs2241841	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241844	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789061	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3789064	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3789065	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3789068	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4302219	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4627572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4849403	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56952027	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60286362	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6708784	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6726007	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs6732491	0.86[JPT][hapmap]
rs6734942	0.90[ASN][1000 genomes]
rs6760053	0.90[JPT][hapmap]
rs7577824	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7593638	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7602904	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv874842	chr2:111870220-111892984	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv829618	chr2:111875627-111881547	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	esv3338590	chr2:111876081-111880479	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv3373707	chr2:111877306-111879854	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv3392605	chr2:111879306-111881854	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111874400-111879800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:111874800-111879600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:111874800-111880000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:111875200-111880000	Bivalent Enhancer	Fetal Brain Male	brain
5	chr2:111875600-111880000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:111875600-111881200	Active TSS	Psoas Muscle	Psoas
7	chr2:111876200-111880000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:111876400-111880000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:111877000-111881000	Active TSS	Small Intestine	intestine
10	chr2:111877000-111881400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:111877200-111880800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr2:111877600-111879800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:111877600-111881000	Active TSS	Esophagus	oesophagus
14	chr2:111877600-111881200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:111877600-111881200	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:111877600-111881400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:111877800-111880000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr2:111877800-111880800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:111877800-111881000	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr2:111877800-111881000	Active TSS	A549	lung
21	chr2:111877800-111881000	Active TSS	Hela-S3	cervix
22	chr2:111877800-111881200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr2:111877800-111881400	Active TSS	Ovary	ovary
24	chr2:111877800-111881400	Active TSS	HSMMtube	muscle
25	chr2:111878000-111879600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:111878000-111879600	Bivalent/Poised TSS	Fetal Thymus	thymus
27	chr2:111878000-111879600	Active TSS	Lung	lung
28	chr2:111878000-111879600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr2:111878000-111880400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr2:111878000-111880800	Active TSS	Primary T cells from cord blood	blood
31	chr2:111878000-111881000	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr2:111878000-111881000	Active TSS	Aorta	Aorta
33	chr2:111878000-111881000	Active TSS	Brain Anterior Caudate	brain
34	chr2:111878000-111881000	Active TSS	Brain Substantia Nigra	brain
35	chr2:111878000-111881000	Active TSS	Gastric	stomach
36	chr2:111878000-111881000	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr2:111878000-111881200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:111878000-111881200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:111878000-111881200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr2:111878000-111881200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr2:111878000-111881200	Active TSS	Fetal Lung	lung
42	chr2:111878000-111881200	Active TSS	Left Ventricle	heart
43	chr2:111878000-111881200	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr2:111878000-111881400	Active TSS	Fetal Kidney	kidney
45	chr2:111878200-111879600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:111878200-111879600	Active TSS	Pancreas	Pancrea
47	chr2:111878200-111880600	Active TSS	Thymus	Thymus
48	chr2:111878200-111880800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:111878200-111880800	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr2:111878200-111880800	Active TSS	Liver	Liver

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