Variant report

Variant	rs28680635
Chromosome Location	chr4:144257079-144257080
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	HCFC1	chr4:144256838-144257773	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr4:144256853-144258635	MCF-7	breast:	n/a	n/a
3	POLR2A	chr4:144257067-144258383	A549	lung:	n/a	n/a
4	CHD2	chr4:144256922-144258211	GM12878	blood:	n/a	chr4:144257188-144257198 chr4:144257525-144257535
5	MAZ	chr4:144256964-144258564	HepG2	liver:	n/a	chr4:144257518-144257528
6	MAX	chr4:144256886-144257810	A549	lung:	n/a	chr4:144257518-144257528 chr4:144256930-144256940
7	POLR2A	chr4:144256855-144258600	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr4:144256938-144258485	PBDE	blood:	n/a	n/a
9	SIN3A	chr4:144256747-144259474	H1-hESC	embryonic stem cell:	n/a	chr4:144258487-144258500
10	YY1	chr4:144256822-144257548	GM12878	blood:	n/a	chr4:144257088-144257096 chr4:144257087-144257099 chr4:144257520-144257529 chr4:144257521-144257532
11	ELF1	chr4:144257021-144257492	K562	blood:	n/a	chr4:144257385-144257397
12	ETS1	chr4:144256990-144257581	A549	lung:	n/a	chr4:144257512-144257523 chr4:144257521-144257532 chr4:144257524-144257535 chr4:144257245-144257258 chr4:144257246-144257259 chr4:144257518-144257529
13	CHD2	chr4:144256822-144258175	Hela-S3	cervix:	n/a	chr4:144257188-144257198 chr4:144257525-144257535
14	EP300	chr4:144257005-144257333	GM12878	blood:	n/a	chr4:144257206-144257215
15	YY1	chr4:144256722-144257705	SK-N-SH	brain:	n/a	chr4:144257088-144257096 chr4:144257663-144257677 chr4:144257087-144257099 chr4:144257520-144257529 chr4:144257521-144257532
16	POLR2A	chr4:144257015-144258619	GM18951	blood:	n/a	n/a
17	POLR2A	chr4:144257042-144257835	A549	lung:	n/a	n/a
18	SIN3AK20	chr4:144256860-144258626	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr4:144257018-144257796	SK-N-SH	brain:	n/a	n/a
20	CHD2	chr4:144256870-144257735	HepG2	liver:	n/a	chr4:144257188-144257198 chr4:144257525-144257535
21	YY1	chr4:144256940-144257449	K562	blood:	n/a	chr4:144257088-144257096 chr4:144257087-144257099
22	CBX3	chr4:144256897-144257695	K562	blood:	n/a	n/a
23	E2F4	chr4:144257059-144257732	MCF10A-Er-Src	breast:	n/a	chr4:144257131-144257143 chr4:144257520-144257529
24	POLR2A	chr4:144257015-144258548	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr4:144256753-144257835	H1-hESC	embryonic stem cell:	n/a	n/a
26	HEY1	chr4:144257019-144257773	K562	blood:	n/a	chr4:144257736-144257751
27	E2F6	chr4:144256894-144257301	A549	lung:	n/a	chr4:144257131-144257143
28	MAX	chr4:144256820-144257729	SK-N-SH	brain:	n/a	chr4:144257518-144257528 chr4:144256930-144256940
29	MXI1	chr4:144257066-144257699	H1-hESC	embryonic stem cell:	n/a	n/a
30	GTF2F1	chr4:144256831-144257473	H1-hESC	embryonic stem cell:	n/a	n/a
31	SIX5	chr4:144257025-144257501	H1-hESC	embryonic stem cell:	n/a	chr4:144257329-144257338
32	TCF12	chr4:144256994-144257846	ECC-1	luminal epithelium:	n/a	n/a
33	BRCA1	chr4:144256931-144257355	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr4:144257033-144258506	GM18526	blood:	n/a	n/a
35	REST	chr4:144257037-144257506	SK-N-SH	brain:	n/a	n/a
36	EP300	chr4:144257011-144257313	GM12878	blood:	n/a	chr4:144257206-144257215
37	TAF1	chr4:144256936-144258470	ECC-1	luminal epithelium:	n/a	n/a
38	JUN	chr4:144256704-144257862	K562	blood:	n/a	n/a
39	MAX	chr4:144256890-144257795	K562	blood:	n/a	chr4:144257518-144257528 chr4:144256930-144256940
40	SP1	chr4:144257048-144257655	A549	lung:	n/a	chr4:144257525-144257537 chr4:144257525-144257537 chr4:144257603-144257615 chr4:144257605-144257614 chr4:144257604-144257618
41	POLR2A	chr4:144256847-144258378	HUVEC	blood vessel:	n/a	n/a
42	NFIC	chr4:144256898-144258510	ECC-1	luminal epithelium:	n/a	n/a
43	CREB1	chr4:144257024-144257488	A549	lung:	n/a	n/a
44	YY1	chr4:144256990-144257351	GM12891	blood:	n/a	chr4:144257088-144257096 chr4:144257087-144257099
45	HNF4A	chr4:144256818-144258256	HepG2	liver:	n/a	chr4:144257990-144258005 chr4:144257649-144257663
46	YY1	chr4:144256681-144257435	H1-hESC	embryonic stem cell:	n/a	chr4:144257088-144257096 chr4:144257087-144257099
47	RAD21	chr4:144257064-144257502	SK-N-SH_RA	brain:	n/a	n/a
48	POLR2A	chr4:144256981-144257811	HepG2	liver:	n/a	n/a
49	FOXP2	chr4:144257035-144257745	PFSK-1	brain:	n/a	n/a
50	CCNT2	chr4:144257041-144259053	K562	blood:	n/a	chr4:144258544-144258553

No.	Distal block	Cell Line	Cell type
1	chr4:144104958..144107554-chr4:144256815..144258504,3	K562	blood:
2	chr4:124524644..124527323-chr4:144255705..144257566,2	MCF-7	breast:
3	chr4:144104818..144107585-chr4:144256509..144260468,4	MCF-7	breast:
4	chr4:144254658..144259448-chr4:144261105..144264742,6	MCF-7	breast:
5	chr4:144254627..144258395-chr4:144297952..144301828,4	K562	blood:
6	chr4:144256474..144260869-chr4:144433151..144436933,4	K562	blood:
7	chr4:144251943..144253888-chr4:144255920..144257556,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FREM3-6	chr4:144256418-144258970	NONHSAT098553

Variant related genes	Relation type
GAB1	TF binding region
ENSG00000265623	Chromatin interaction
ENSG00000245112	Chromatin interaction
ENSG00000153147	Chromatin interaction
ENSG00000170185	Chromatin interaction
ENSG00000109458	Chromatin interaction
ENSG00000250326	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17017563	1.00[ASN][1000 genomes]
rs17017629	1.00[ASN][1000 genomes]
rs17017662	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28377860	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448391	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676298	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825973	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947118	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv3332574	chr4:144239396-144259577	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	esv3406126	chr4:144256927-144259675	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144256000-144259600	Active TSS	Fetal Kidney	kidney
2	chr4:144256200-144257200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr4:144256200-144259000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:144256600-144257200	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr4:144256600-144257200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:144256600-144257400	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr4:144256600-144257400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr4:144256600-144257600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:144256600-144258600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:144256600-144258600	Active TSS	Fetal Muscle Trunk	muscle
11	chr4:144256600-144258800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr4:144256600-144258800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:144256600-144258800	Active TSS	Liver	Liver
14	chr4:144256600-144258800	Active TSS	Hela-S3	cervix
15	chr4:144256600-144259000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:144256600-144259000	Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr4:144256600-144259000	Active TSS	HMEC	breast
18	chr4:144256600-144259000	Active TSS	HUVEC	blood vessel
19	chr4:144256600-144259000	Active TSS	NH-A	brain
20	chr4:144256600-144259000	Active TSS	NHEK	skin
21	chr4:144256600-144259000	Active TSS	Osteobl	bone
22	chr4:144256600-144259200	Active TSS	H1 Cell Line	embryonic stem cell
23	chr4:144256600-144259200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:144256600-144259200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:144256600-144259200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr4:144256600-144259200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr4:144256600-144259200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr4:144256600-144259200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:144256600-144259200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:144256600-144259200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:144256600-144259200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:144256600-144259200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:144256600-144259400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr4:144256600-144259400	Active TSS	H9 Cell Line	embryonic stem cell
35	chr4:144256600-144259400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:144256600-144259400	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr4:144256600-144259400	Active TSS	Primary T cells from cord blood	blood
38	chr4:144256600-144259400	Active TSS	Fetal Lung	lung
39	chr4:144256600-144259400	Active TSS	A549	lung
40	chr4:144256600-144259400	Active TSS	HSMMtube	muscle
41	chr4:144256600-144259600	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr4:144256600-144259600	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr4:144256600-144259600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:144256600-144259600	Active TSS	Psoas Muscle	Psoas
45	chr4:144256600-144259600	Active TSS	Rectal Smooth Muscle	rectum
46	chr4:144256600-144259600	Active TSS	Stomach Smooth Muscle	stomach
47	chr4:144256600-144259800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:144256600-144259800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:144256600-144259800	Active TSS	Colon Smooth Muscle	Colon
50	chr4:144256600-144259800	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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