Variant report

Variant	rs2306941
Chromosome Location	chr1:179198653-179198654
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	TAF1	chr1:179198051-179199154	HepG2	liver:	n/a	n/a
2	SMARCB1	chr1:179197960-179199297	Hela-S3	cervix:	n/a	n/a
3	MAX	chr1:179198376-179199385	MCF-7	breast:	n/a	chr1:179199191-179199198
4	YY1	chr1:179198172-179199261	SK-N-SH	brain:	n/a	chr1:179198587-179198601 chr1:179198794-179198811 chr1:179198554-179198563 chr1:179198228-179198248 chr1:179198201-179198212 chr1:179198669-179198683 chr1:179198689-179198700 chr1:179198229-179198248 chr1:179198654-179198668
5	POLR2A	chr1:179198513-179198822	ECC-1	luminal epithelium:	n/a	n/a
6	ZKSCAN1	chr1:179198527-179198716	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:179198324-179199341	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr1:179198511-179199220	K562	blood:	n/a	n/a
9	TEAD4	chr1:179198386-179198779	H1-hESC	embryonic stem cell:	n/a	chr1:179198574-179198583
10	POLR2A	chr1:179198489-179198821	A549	lung:	n/a	n/a
11	POLR2A	chr1:179198607-179198825	HepG2	liver:	n/a	n/a
12	SIN3A	chr1:179197840-179199404	H1-hESC	embryonic stem cell:	n/a	chr1:179198604-179198613
13	POLR2A	chr1:179198562-179198841	HCT-116	colon:	n/a	n/a
14	MYC	chr1:179198066-179200154	K562	blood:	n/a	chr1:179199609-179199619 chr1:179198329-179198339 chr1:179199610-179199617 chr1:179199607-179199620 chr1:179199609-179199618 chr1:179198198-179198208 chr1:179199608-179199618 chr1:179199605-179199620 chr1:179199191-179199198 chr1:179199610-179199619 chr1:179199607-179199622 chr1:179199608-179199619
15	POLR2A	chr1:179198422-179198882	ECC-1	luminal epithelium:	n/a	n/a
16	MAZ	chr1:179197859-179199300	Hela-S3	cervix:	n/a	chr1:179198329-179198339 chr1:179198198-179198208 chr1:179199191-179199198
17	POLR2A	chr1:179198418-179198808	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:179198448-179198653	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:179198402-179199210	HepG2	liver:	n/a	n/a
20	TAF1	chr1:179198407-179198924	ECC-1	luminal epithelium:	n/a	n/a
21	ZEB1	chr1:179198314-179199469	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:179198605-179199082	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:179198390-179199189	A549	lung:	n/a	n/a
24	HEY1	chr1:179198511-179198860	K562	blood:	n/a	chr1:179198693-179198708
25	POLR2A	chr1:179198494-179198827	A549	lung:	n/a	n/a
26	YY1	chr1:179198377-179199166	SK-N-SH_RA	brain:	n/a	chr1:179198587-179198601 chr1:179198794-179198811 chr1:179198554-179198563 chr1:179198669-179198683 chr1:179198689-179198700 chr1:179198654-179198668
27	TBP	chr1:179198482-179198850	H1-hESC	embryonic stem cell:	n/a	n/a
28	UBTF	chr1:179197783-179199168	K562	blood:	n/a	n/a
29	MAX	chr1:179197942-179199881	HCT-116	colon:	n/a	chr1:179199609-179199619 chr1:179198329-179198339 chr1:179199610-179199617 chr1:179199607-179199620 chr1:179199609-179199618 chr1:179198198-179198208 chr1:179199608-179199618 chr1:179199605-179199620 chr1:179199191-179199198 chr1:179199610-179199619 chr1:179199607-179199622 chr1:179199608-179199619
30	CCNT2	chr1:179198363-179198791	K562	blood:	n/a	n/a
31	YY1	chr1:179198406-179198869	HepG2	liver:	n/a	chr1:179198587-179198601 chr1:179198794-179198811 chr1:179198554-179198563 chr1:179198669-179198683 chr1:179198689-179198700 chr1:179198654-179198668
32	YY1	chr1:179198400-179198918	GM12892	blood:	n/a	chr1:179198587-179198601 chr1:179198794-179198811 chr1:179198554-179198563 chr1:179198669-179198683 chr1:179198689-179198700 chr1:179198654-179198668
33	JUND	chr1:179198604-179198740	K562	blood:	n/a	n/a
34	POLR2A	chr1:179198099-179199311	Raji	blood:	n/a	n/a
35	EGR1	chr1:179198424-179198695	K562	blood:	n/a	chr1:179198552-179198565
36	TAF1	chr1:179198250-179198974	K562	blood:	n/a	n/a
37	POLR2A	chr1:179198582-179198843	A549	lung:	n/a	n/a
38	MXI1	chr1:179197473-179200615	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr1:179198167-179199291	MCF-7	breast:	n/a	n/a
40	MXI1	chr1:179198120-179199366	HepG2	liver:	n/a	n/a
41	CHD1	chr1:179198345-179198918	IMR90	lung:	n/a	chr1:179198754-179198764
42	EP300	chr1:179198384-179199010	ECC-1	luminal epithelium:	n/a	chr1:179198684-179198700
43	ZBTB7A	chr1:179198333-179199443	ECC-1	luminal epithelium:	n/a	chr1:179198757-179198766
44	MAX	chr1:179197803-179199334	HepG2	liver:	n/a	chr1:179198329-179198339 chr1:179198198-179198208 chr1:179199191-179199198
45	POLR2A	chr1:179198489-179198848	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:179198508-179198803	GM12892	blood:	n/a	n/a
47	YY1	chr1:179198328-179198926	GM12891	blood:	n/a	chr1:179198587-179198601 chr1:179198794-179198811 chr1:179198554-179198563 chr1:179198669-179198683 chr1:179198689-179198700 chr1:179198654-179198668
48	MAX	chr1:179198519-179199509	ECC-1	luminal epithelium:	n/a	chr1:179199191-179199198
49	POLR2A	chr1:179198388-179199181	GM18951	blood:	n/a	n/a
50	TAF1	chr1:179198406-179198850	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179198544..179200421-chr1:179334252..179336417,2	MCF-7	breast:
2	chr1:179189295..179193775-chr1:179196197..179201101,5	K562	blood:
3	chr1:179188599..179190144-chr1:179197953..179200570,2	MCF-7	breast:
4	chr1:179168461..179170793-chr1:179198127..179200126,2	MCF-7	breast:
5	chr1:179187242..179191261-chr1:179196503..179201085,5	MCF-7	breast:

Variant related genes	Relation type
ABL2	TF binding region
ENSG00000225711	Chromatin interaction
ENSG00000162779	Chromatin interaction
ENSG00000201619	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1078872	0.86[ASN][1000 genomes]
rs12132572	0.80[ASN][1000 genomes]
rs1763022	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1807916	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1826183	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2050923	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066279	0.87[ASN][1000 genomes]
rs2130576	0.87[ASN][1000 genomes]
rs2171958	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2486998	0.82[EUR][1000 genomes]
rs2487563	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636265	0.87[ASN][1000 genomes]
rs2636272	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2636277	0.85[EUR][1000 genomes]
rs2636280	0.83[ASN][1000 genomes]
rs2636282	0.87[ASN][1000 genomes]
rs2636291	0.81[EUR][1000 genomes]
rs2791936	0.85[EUR][1000 genomes]
rs2791944	0.81[EUR][1000 genomes]
rs2791945	0.91[EUR][1000 genomes]
rs2793790	0.85[EUR][1000 genomes]
rs2793794	0.84[EUR][1000 genomes]
rs2793800	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2793801	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2793802	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2793803	0.88[ASN][1000 genomes]
rs2793810	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2793812	0.83[ASN][1000 genomes]
rs2793813	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2816166	0.83[EUR][1000 genomes]
rs2816168	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2816184	0.85[EUR][1000 genomes]
rs2816191	0.86[EUR][1000 genomes]
rs2816197	0.83[ASN][1000 genomes]
rs2816198	0.83[ASN][1000 genomes]
rs2816199	0.83[ASN][1000 genomes]
rs2816200	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2816201	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2816202	0.83[ASN][1000 genomes]
rs2816203	0.82[ASN][1000 genomes]
rs2816204	0.82[ASN][1000 genomes]
rs2816207	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2816208	0.87[ASN][1000 genomes]
rs2816211	0.88[ASN][1000 genomes]
rs2816212	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2816214	0.87[ASN][1000 genomes]
rs2816218	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3121198	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3122376	0.81[ASN][1000 genomes]
rs377785	0.86[ASN][1000 genomes]
rs411266	0.86[ASN][1000 genomes]
rs413613	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs434283	0.86[ASN][1000 genomes]
rs451088	0.86[ASN][1000 genomes]
rs915337	0.86[ASN][1000 genomes]
rs9286921	0.81[EUR][1000 genomes]
rs9425839	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9729129	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3441716	chr1:179197554-179200302	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 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	chr1:179197400-179199000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:179197400-179199400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:179197600-179199000	Active TSS	Colonic Mucosa	Colon
4	chr1:179197600-179199000	Active TSS	Fetal Muscle Trunk	muscle
5	chr1:179197600-179199400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:179197600-179199400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:179197600-179199400	Active TSS	Aorta	Aorta
8	chr1:179197600-179199400	Active TSS	Right Atrium	heart
9	chr1:179197600-179199800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:179197600-179199800	Active TSS	NHLF	lung
11	chr1:179197800-179199000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:179197800-179199200	Active TSS	Fetal Intestine Large	intestine
13	chr1:179197800-179199400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr1:179197800-179199400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:179197800-179199400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:179197800-179199400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:179197800-179199400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr1:179197800-179199400	Active TSS	Esophagus	oesophagus
19	chr1:179197800-179199400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:179197800-179199400	Active TSS	Placenta	Placenta
21	chr1:179197800-179199400	Active TSS	Left Ventricle	heart
22	chr1:179197800-179199400	Active TSS	Ovary	ovary
23	chr1:179197800-179199400	Active TSS	Psoas Muscle	Psoas
24	chr1:179197800-179199400	Active TSS	A549	lung
25	chr1:179197800-179199600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:179198000-179198800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:179198000-179199000	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:179198000-179199000	Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:179198000-179199000	Active TSS	Brain Cingulate Gyrus	brain
30	chr1:179198000-179199000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr1:179198000-179199000	Active TSS	HMEC	breast
32	chr1:179198000-179199200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr1:179198000-179199200	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr1:179198000-179199200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:179198000-179199200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:179198000-179199200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:179198000-179199200	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:179198000-179199200	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr1:179198000-179199200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:179198000-179199200	Active TSS	Brain Hippocampus Middle	brain
41	chr1:179198000-179199200	Active TSS	Brain Substantia Nigra	brain
42	chr1:179198000-179199200	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr1:179198000-179199200	Active TSS	Spleen	Spleen
44	chr1:179198000-179199200	Active TSS	Hela-S3	cervix
45	chr1:179198000-179199200	Active TSS	HepG2	liver
46	chr1:179198000-179199200	Active TSS	K562	blood
47	chr1:179198000-179199200	Active TSS	Osteobl	bone
48	chr1:179198000-179199400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:179198000-179199400	Active TSS	H9 Cell Line	embryonic stem cell
50	chr1:179198000-179199400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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