Variant report

Variant	rs10145379
Chromosome Location	chr14:38065813-38065814
allele	G/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	POLR2A	chr14:38064025-38065942	HepG2	liver:	n/a	n/a
2	E2F6	chr14:38065208-38065851	K562	blood:	n/a	chr14:38065392-38065404 chr14:38065519-38065531 chr14:38065520-38065531 chr14:38065518-38065533
3	HDAC2	chr14:38064385-38065999	MCF-7	breast:	n/a	chr14:38064764-38064778 chr14:38065036-38065050 chr14:38065033-38065047 chr14:38065035-38065049 chr14:38064765-38064779
4	MBD4	chr14:38062469-38066000	HepG2	liver:	n/a	n/a
5	TCF12	chr14:38064333-38065905	A549	lung:	n/a	chr14:38065551-38065559
6	POLR2A	chr14:38063610-38065883	MCF-7	breast:	n/a	n/a
7	ARID3A	chr14:38062570-38065874	HepG2	liver:	n/a	n/a
8	POLR2A	chr14:38064708-38065831	HepG2	liver:	n/a	n/a
9	MYC	chr14:38065777-38065848	HepG2	liver:	n/a	n/a
10	RFX5	chr14:38063390-38065891	HepG2	liver:	n/a	n/a
11	POLR2A	chr14:38063223-38065902	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:38062953-38066652	MCF10A-Er-Src	breast:	n/a	n/a
13	RCOR1	chr14:38063421-38066027	HepG2	liver:	n/a	n/a
14	HA-E2F1	chr14:38063407-38065989	MCF-7	breast:	n/a	chr14:38065392-38065404 chr14:38065519-38065531 chr14:38065518-38065533 chr14:38064782-38064792
15	RAD21	chr14:38064596-38065827	MCF-7	breast:	n/a	n/a
16	JUND	chr14:38062628-38066066	MCF-7	breast:	n/a	chr14:38064795-38064804 chr14:38065116-38065126 chr14:38063103-38063111 chr14:38065214-38065223 chr14:38063106-38063118 chr14:38064080-38064089 chr14:38065116-38065126 chr14:38062672-38062682 chr14:38065212-38065223 chr14:38065116-38065126 chr14:38064791-38064800 chr14:38063103-38063110 chr14:38065396-38065405 chr14:38065116-38065126 chr14:38063967-38063976 chr14:38065213-38065222
17	POLR2A	chr14:38065581-38065961	H1-neurons	neurons:	n/a	n/a
18	NR2F2	chr14:38063222-38066101	MCF-7	breast:	n/a	n/a
19	SIN3AK20	chr14:38060259-38066080	MCF-7	breast:	n/a	n/a
20	MAX	chr14:38063265-38066034	HepG2	liver:	n/a	chr14:38064741-38064751
21	GATA3	chr14:38064013-38066440	MCF-7	breast:	n/a	chr14:38066429-38066436
22	REST	chr14:38064753-38065924	A549	lung:	n/a	chr14:38065269-38065282
23	TBP	chr14:38064073-38065842	K562	blood:	n/a	n/a
24	POLR2A	chr14:38063785-38065819	HepG2	liver:	n/a	n/a
25	GATA3	chr14:38063996-38065914	T-47D	breast:	n/a	n/a
26	GATA3	chr14:38063361-38065823	MCF-7	breast:	n/a	n/a
27	GATA3	chr14:38065023-38065981	T-47D	breast:	n/a	n/a
28	ZNF263	chr14:38062768-38066049	HEK293-T-REx	kidney:	n/a	chr14:38065390-38065399 chr14:38064974-38064983
29	MAX	chr14:38065203-38065878	K562	blood:	n/a	n/a
30	POLR2A	chr14:38064339-38065913	HepG2	liver:	n/a	n/a
31	MAX	chr14:38064007-38066194	MCF-7	breast:	n/a	chr14:38064741-38064751
32	E2F6	chr14:38065205-38065918	A549	lung:	n/a	chr14:38065392-38065404 chr14:38065519-38065531 chr14:38065520-38065531 chr14:38065518-38065533
33	MAX	chr14:38063390-38065930	HepG2	liver:	n/a	chr14:38064741-38064751
34	POLR2A	chr14:38064149-38065862	HepG2	liver:	n/a	n/a
35	MAX	chr14:38063221-38065953	A549	lung:	n/a	chr14:38064741-38064751
36	EP300	chr14:38062686-38065992	MCF-7	breast:	n/a	chr14:38063806-38063822 chr14:38063793-38063809 chr14:38064922-38064938 chr14:38065416-38065429
37	CEBPD	chr14:38063986-38065839	HepG2	liver:	n/a	n/a
38	TBP	chr14:38064066-38065951	HepG2	liver:	n/a	n/a
39	POLR2A	chr14:38063297-38066604	HepG2	liver:	n/a	n/a
40	MAX	chr14:38063166-38066136	HepG2	liver:	n/a	chr14:38064741-38064751
41	TCF12	chr14:38064336-38065910	MCF-7	breast:	n/a	chr14:38065551-38065559
42	MYC	chr14:38064119-38065998	K562	blood:	n/a	chr14:38064741-38064751
43	POLR2A	chr14:38065620-38066065	H1-neurons	neurons:	n/a	n/a
44	SUZ12	chr14:38063382-38065945	NT2-D1	testis:	n/a	n/a
45	MAX	chr14:38065307-38065871	A549	lung:	n/a	n/a
46	POLR2A	chr14:38063827-38065860	K562	blood:	n/a	n/a
47	TAF1	chr14:38063219-38065949	MCF-7	breast:	n/a	n/a
48	MAX	chr14:38063185-38066099	MCF-7	breast:	n/a	chr14:38064741-38064751
49	FOSL2	chr14:38063983-38065909	HepG2	liver:	n/a	chr14:38064795-38064804 chr14:38065116-38065126 chr14:38065214-38065223 chr14:38064080-38064089 chr14:38065116-38065126 chr14:38065116-38065126 chr14:38064791-38064800 chr14:38065396-38065405 chr14:38065116-38065126 chr14:38065213-38065222
50	TAF1	chr14:38063211-38065977	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:7053819..7056575-chr14:38063408..38066179,2	MCF-7	breast:
2	chr14:38065586..38067163-chr17:59765221..59767860,2	MCF-7	breast:
3	chr14:38065320..38065829-chr14:38119737..38120477,2	MCF-7	breast:
4	chr14:38065477..38068089-chr14:38070439..38072783,2	K562	blood:
5	chr14:38064575..38066712-chr14:38067823..38069498,2	K562	blood:
6	chr14:38063715..38066524-chr16:54963024..54965693,2	MCF-7	breast:
7	chr14:37709149..37730989-chr14:38048141..38067789,135	MCF-7	breast:
8	chr14:38065742..38067399-chr6:13813681..13815787,2	MCF-7	breast:
9	chr1:249152224..249152732-chr14:38065328..38065950,2	MCF-7	breast:
10	chr14:37708906..37733371-chr14:38048131..38068843,170	MCF-7	breast:
11	chr14:38064027..38066439-chr20:52209479..52211136,2	MCF-7	breast:
12	chr14:38065415..38067137-chr5:156264279..156265799,2	MCF-7	breast:
13	chr14:38035755..38036301-chr14:38065026..38065953,2	MCF-7	breast:
14	chr14:38064151..38065863-chr2:43452314..43453931,2	MCF-7	breast:
15	chr14:37667184..37668809-chr14:38065579..38068114,2	MCF-7	breast:
16	chr14:37641087..37642667-chr14:38063502..38066629,3	MCF-7	breast:

Variant related genes	Relation type
FOXA1	TF binding region
ENSG00000129514	Chromatin interaction
ENSG00000259087	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000111679	Chromatin interaction
ENSG00000151338	Chromatin interaction
ENSG00000258708	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000176842	Chromatin interaction
ENSG00000050393	Chromatin interaction
ENSG00000245694	Chromatin interaction
ENSG00000171163	Chromatin interaction
ENSG00000183032	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1008236	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs10133438	0.86[CHB][hapmap]
rs10143976	0.91[CHD][hapmap]
rs10144334	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10145473	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10151200	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs10400689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs1057536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11156961	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs11156962	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs1155456	0.91[CHD][hapmap]
rs1158701	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs1159151	0.86[CHB][hapmap]
rs11623989	0.87[CHD][hapmap]
rs11627807	0.97[ASN][1000 genomes]
rs11627844	0.81[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1169873	0.91[CHD][hapmap]
rs11846416	0.85[ASN][1000 genomes]
rs12147939	0.83[CEU][hapmap]
rs12884884	0.82[GIH][hapmap]
rs12894536	0.83[CHD][hapmap]
rs12896760	0.83[CHD][hapmap]
rs1547009	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs17179078	0.83[CHD][hapmap]
rs17768249	0.83[CHD][hapmap]
rs17768343	0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1814005	0.91[CHD][hapmap]
rs1884798	0.87[ASN][1000 genomes]
rs1884803	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1950824	0.87[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs1950826	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs1955934	0.87[CHD][hapmap]
rs1955943	0.83[CHD][hapmap]
rs1956427	0.91[CHD][hapmap]
rs1956429	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1956433	0.91[CHD][hapmap]
rs1956437	0.91[CHD][hapmap]
rs1956442	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1956443	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1980675	0.88[CEU][hapmap];0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs2006729	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs2146133	0.91[CHD][hapmap]
rs2180609	0.91[CHD][hapmap]
rs2415404	0.91[CHD][hapmap]
rs4900918	0.91[CHD][hapmap]
rs4900945	0.91[CHD][hapmap]
rs4900958	0.80[CEU][hapmap]
rs4900969	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap]
rs4901012	0.92[ASN][1000 genomes]
rs6571812	0.83[CHD][hapmap]
rs6571814	0.91[CHD][hapmap]
rs7144658	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145671	0.83[CHD][hapmap]
rs7146299	0.91[CHD][hapmap]
rs7146958	0.85[ASN][1000 genomes]
rs7147379	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7153426	0.91[CHD][hapmap]
rs7153867	0.85[ASN][1000 genomes]
rs7159456	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs7160774	0.92[ASN][1000 genomes]
rs7161228	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161326	0.90[CHD][hapmap]
rs7493775	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs762083	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8005136	0.91[CHD][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs8008655	0.83[CHD][hapmap]
rs8016138	0.85[ASN][1000 genomes]
rs8019713	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs9322981	0.83[ASN][1000 genomes]
rs968350	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs996916	0.86[CHB][hapmap];0.91[CHD][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530038	chr14:37590543-38336191	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv826923	chr14:38017619-38108645	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv832772	chr14:38030300-38225921	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv901642	chr14:38041870-38081005	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv901643	chr14:38047789-38081005	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	nsv901646	chr14:38051035-38081005	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv901648	chr14:38052110-38065813	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
9	nsv901649	chr14:38053334-38065813	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	esv3405207	chr14:38062726-38066074	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10145379	SEC23A	cis	parietal	SCAN
rs10145379	BRMS1L	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38056400-38066000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
2	chr14:38064400-38066400	Bivalent/Poised TSS	Colonic Mucosa	Colon
3	chr14:38064800-38066000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
4	chr14:38064800-38066200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
5	chr14:38064800-38066800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
6	chr14:38065000-38066000	Bivalent/Poised TSS	Fetal Lung	lung
7	chr14:38065000-38066800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr14:38065000-38069600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
9	chr14:38065200-38066800	Bivalent/Poised TSS	Fetal Stomach	stomach
10	chr14:38065400-38066000	Flanking Active TSS	Liver	Liver
11	chr14:38065400-38066000	Flanking Active TSS	Hela-S3	cervix
12	chr14:38065600-38066000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
13	chr14:38065600-38066000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
14	chr14:38065600-38066000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr14:38065600-38066000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr14:38065600-38066600	Flanking Active TSS	A549	lung
17	chr14:38065600-38067000	Weak transcription	Lung	lung
18	chr14:38065600-38067000	Weak transcription	Pancreas	Pancrea
19	chr14:38065800-38066000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr14:38065800-38066000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:38065800-38066000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr14:38065800-38066000	Enhancers	K562	blood
23	chr14:38065800-38066000	Bivalent Enhancer	NHEK	skin
24	chr14:38065800-38066400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
25	chr14:38065800-38066600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr14:38065800-38066600	Flanking Active TSS	HepG2	liver
27	chr14:38065800-38066800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
28	chr14:38065800-38067000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:38065800-38067000	Weak transcription	Esophagus	oesophagus
30	chr14:38065800-38067200	Weak transcription	Gastric	stomach
31	chr14:38065800-38067600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
32	chr14:38065800-38068800	Bivalent Enhancer	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links