Variant report

Variant	rs2276975
Chromosome Location	chr4:104119587-104119588
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	BHLHE40	chr4:104119284-104120139	HepG2	liver:	n/a	n/a
2	YY1	chr4:104119341-104119772	ECC-1	luminal epithelium:	n/a	chr4:104119502-104119512 chr4:104119371-104119380 chr4:104119365-104119379
3	POLR2A	chr4:104119269-104119634	A549	lung:	n/a	n/a
4	BHLHE40	chr4:104119489-104119835	A549	lung:	n/a	n/a
5	NR2F2	chr4:104118928-104119860	K562	blood:	n/a	n/a
6	CREB1	chr4:104118773-104120136	K562	blood:	n/a	chr4:104119604-104119617
7	POLR2A	chr4:104118978-104120073	MCF-7	breast:	n/a	n/a
8	JUND	chr4:104119259-104119897	H1-hESC	embryonic stem cell:	n/a	chr4:104119653-104119662 chr4:104119606-104119615 chr4:104119546-104119555
9	POLR2A	chr4:104119168-104119767	MCF-7	breast:	n/a	n/a
10	POLR2A	chr4:104119105-104119792	Hela-S3	cervix:	n/a	n/a
11	YY1	chr4:104119011-104119792	K562	blood:	n/a	chr4:104119502-104119512 chr4:104119371-104119380 chr4:104119365-104119379
12	SP1	chr4:104119379-104119893	GM12878	blood:	n/a	chr4:104119548-104119559
13	USF1	chr4:104119420-104119707	H1-hESC	embryonic stem cell:	n/a	chr4:104119600-104119611
14	USF2	chr4:104119417-104119836	GM12878	blood:	n/a	n/a
15	EGR1	chr4:104119559-104119742	GM12878	blood:	n/a	n/a
16	EP300	chr4:104119386-104119952	GM12878	blood:	n/a	chr4:104119654-104119663
17	RFX5	chr4:104119439-104120030	GM12878	blood:	n/a	n/a
18	MAX	chr4:104119444-104119782	K562	blood:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
19	MAZ	chr4:104119268-104119778	Hela-S3	cervix:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
20	HCFC1	chr4:104118967-104119863	K562	blood:	n/a	n/a
21	ZBTB7A	chr4:104119169-104119860	ECC-1	luminal epithelium:	n/a	n/a
22	USF1	chr4:104119429-104119749	A549	lung:	n/a	chr4:104119600-104119611
23	CHD1	chr4:104119393-104119885	H1-hESC	embryonic stem cell:	n/a	n/a
24	SP1	chr4:104119359-104119749	H1-hESC	embryonic stem cell:	n/a	chr4:104119548-104119559
25	TAF1	chr4:104119214-104119662	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr4:104119343-104120110	K562	blood:	n/a	n/a
27	ETS1	chr4:104119238-104119816	K562	blood:	n/a	n/a
28	POLR2A	chr4:104119055-104119916	HEK293	kidney:	n/a	n/a
29	SIN3AK20	chr4:104118930-104119945	HCT-116	colon:	n/a	n/a
30	IRF1	chr4:104119129-104119887	K562	blood:	n/a	n/a
31	MAX	chr4:104118911-104119905	MCF-7	breast:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
32	POLR2A	chr4:104118962-104119804	ProgFib	skin:	n/a	n/a
33	POLR2A	chr4:104119338-104119626	GM12892	blood:	n/a	n/a
34	MAX	chr4:104118948-104119845	K562	blood:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
35	SP4	chr4:104119490-104119802	H1-hESC	embryonic stem cell:	n/a	chr4:104119548-104119559
36	E2F4	chr4:104119063-104119812	K562	blood:	n/a	chr4:104119605-104119614 chr4:104119607-104119616
37	POLR2A	chr4:104118975-104119811	K562	blood:	n/a	n/a
38	POLR2A	chr4:104119190-104119604	GM12878	blood:	n/a	n/a
39	EP300	chr4:104119200-104119953	H1-hESC	embryonic stem cell:	n/a	chr4:104119371-104119380 chr4:104119654-104119663
40	CREB1	chr4:104119198-104120112	HepG2	liver:	n/a	chr4:104119604-104119617
41	CBX3	chr4:104119119-104120149	K562	blood:	n/a	n/a
42	CEBPB	chr4:104119386-104119741	HepG2	liver:	n/a	n/a
43	JUND	chr4:104119311-104119772	H1-hESC	embryonic stem cell:	n/a	chr4:104119653-104119662 chr4:104119606-104119615 chr4:104119546-104119555
44	SIN3AK20	chr4:104118984-104119664	H1-hESC	embryonic stem cell:	n/a	n/a
45	SIX5	chr4:104119337-104120076	A549	lung:	n/a	n/a
46	JUND	chr4:104119508-104119709	HepG2	liver:	n/a	chr4:104119653-104119662 chr4:104119606-104119615 chr4:104119546-104119555
47	MAX	chr4:104118936-104119988	SK-N-SH	brain:	n/a	chr4:104119624-104119631 chr4:104119623-104119632
48	ZBTB7A	chr4:104119231-104119828	K562	blood:	n/a	n/a
49	POLR2A	chr4:104119105-104119817	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr4:104119059-104120019	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:100741160..100741678-chr4:104118965..104119923,2	HCT-116	colon:

Variant related genes	Relation type
CENPE	TF binding region
ENSG00000175198	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10516497	0.86[CEU][hapmap]
rs11734396	0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12502620	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12505012	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12506575	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17033423	0.88[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17217250	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17283278	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243682	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290943	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2615538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2615541	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2615542	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623062	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623063	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623069	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623076	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623082	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711888	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711889	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711891	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2711893	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711894	0.80[AMR][1000 genomes]
rs2711895	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2711896	0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711900	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2711901	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720447	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720449	0.93[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720451	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720452	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720453	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720455	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720456	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720457	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720463	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720465	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720467	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720470	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816642	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698879	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55708783	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55777543	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59355472	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68023422	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6830082	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847142	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847357	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665085	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72665089	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72666813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7435875	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7672974	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9760911	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830022	chr4:104087199-104257784	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr4:104117800-104120200	Active TSS	NHDF-Ad	bronchial
2	chr4:104118000-104120000	Active TSS	A549	lung
3	chr4:104118000-104120200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr4:104118000-104120200	Active TSS	GM12878-XiMat	blood
5	chr4:104118000-104120400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:104118000-104120400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:104118000-104120400	Active TSS	NHLF	lung
8	chr4:104118200-104119600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:104118200-104119800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:104118200-104119800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:104118200-104120000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr4:104118200-104120200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:104118200-104120200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:104118200-104120200	Active TSS	Fetal Brain Male	brain
15	chr4:104118200-104120200	Active TSS	K562	blood
16	chr4:104118200-104120400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:104118200-104120400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:104118400-104119600	Active TSS	Fetal Muscle Trunk	muscle
19	chr4:104118400-104119800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:104118400-104120000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:104118400-104120000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:104118400-104120200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:104118400-104120200	Active TSS	HSMMtube	muscle
24	chr4:104118400-104120200	Active TSS	Osteobl	bone
25	chr4:104118400-104120400	Active TSS	HSMM	muscle
26	chr4:104118600-104119600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:104118600-104119800	Active TSS	HMEC	breast
28	chr4:104118600-104120000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr4:104118600-104120000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:104118600-104120000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:104118600-104120000	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr4:104118600-104120000	Active TSS	Fetal Intestine Large	intestine
33	chr4:104118600-104120200	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr4:104118600-104120200	Active TSS	H9 Cell Line	embryonic stem cell
35	chr4:104118600-104120200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:104118600-104120200	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr4:104118600-104120200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:104118600-104120200	Active TSS	Hela-S3	cervix
39	chr4:104118600-104120400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:104118600-104120400	Active TSS	Fetal Muscle Leg	muscle
41	chr4:104118800-104119800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:104118800-104119800	Active TSS	Dnd41	blood
43	chr4:104118800-104119800	Active TSS	HUVEC	blood vessel
44	chr4:104118800-104119800	Active TSS	NH-A	brain
45	chr4:104118800-104120000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:104118800-104120000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:104118800-104120000	Active TSS	Muscle Satellite Cultured Cells	--
48	chr4:104118800-104120000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:104118800-104120000	Active TSS	Fetal Heart	heart
50	chr4:104118800-104120200	Active TSS	HUES64 Cell Line	embryonic stem cell

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