Variant report

Variant	rs1953416
Chromosome Location	chr14:65878807-65878808
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	CEBPD	chr14:65878507-65878869	HepG2	liver:	n/a	n/a
2	TAF1	chr14:65878277-65879597	MCF-7	breast:	n/a	n/a
3	ZNF263	chr14:65878053-65879887	HEK293-T-REx	kidney:	n/a	n/a
4	POLR2A	chr14:65878319-65880001	A549	lung:	n/a	n/a
5	JUND	chr14:65878219-65879554	MCF-7	breast:	n/a	chr14:65878509-65878518 chr14:65878550-65878559
6	RELA	chr14:65878467-65879932	GM18951	blood:	n/a	n/a
7	CTCF	chr14:65878740-65878890	GM12878	blood:	n/a	n/a
8	TBP	chr14:65878226-65879498	Hela-S3	cervix:	n/a	n/a
9	SIN3AK20	chr14:65878148-65880348	MCF-7	breast:	n/a	n/a
10	POLR2A	chr14:65878315-65879844	HUVEC	blood vessel:	n/a	n/a
11	RELA	chr14:65878258-65879928	GM15510	blood:	n/a	n/a
12	POLR2A	chr14:65877779-65880666	GM12892	blood:	n/a	n/a
13	GTF3C2	chr14:65878260-65879067	Hela-S3	cervix:	n/a	n/a
14	TAF1	chr14:65878344-65880520	H1-neurons	neurons:	n/a	n/a
15	MXI1	chr14:65878527-65879876	HepG2	liver:	n/a	n/a
16	RAD21	chr14:65878439-65879917	MCF-7	breast:	n/a	chr14:65879378-65879390 chr14:65879191-65879210
17	MAZ	chr14:65878366-65880367	Hela-S3	cervix:	n/a	chr14:65879334-65879344
18	POLR2A	chr14:65878080-65880573	Raji	blood:	n/a	n/a
19	CTBP2	chr14:65878437-65880458	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr14:65877745-65880761	GM12892	blood:	n/a	n/a
21	FOXA2	chr14:65878594-65878906	HepG2	liver:	n/a	n/a
22	POLR2A	chr14:65878308-65879548	GM12891	blood:	n/a	n/a
23	NFATC1	chr14:65878330-65879548	GM12878	blood:	n/a	n/a
24	POLR2A	chr14:65877470-65881012	GM12891	blood:	n/a	n/a
25	POLR2A	chr14:65877799-65880930	GM12878	blood:	n/a	n/a
26	E2F6	chr14:65878374-65878819	H1-hESC	embryonic stem cell:	n/a	chr14:65878601-65878610 chr14:65878511-65878520
27	RELA	chr14:65878067-65879970	GM10847	blood:	n/a	n/a
28	MYC	chr14:65878401-65879889	NB4	blood:	n/a	chr14:65879334-65879344
29	RAD21	chr14:65878068-65880004	MCF-7	breast:	n/a	chr14:65879378-65879390 chr14:65879191-65879210
30	RFX5	chr14:65878314-65879835	Hela-S3	cervix:	n/a	chr14:65878551-65878560 chr14:65878510-65878519
31	POLR2A	chr14:65877789-65880853	GM19099	blood:	n/a	n/a
32	CTCF	chr14:65878429-65879928	GM12878	blood:	n/a	n/a
33	RAD21	chr14:65878221-65879550	H1-hESC	embryonic stem cell:	n/a	chr14:65879378-65879390 chr14:65879191-65879210
34	ELF1	chr14:65878141-65880025	MCF-7	breast:	n/a	chr14:65879763-65879775 chr14:65878779-65878788 chr14:65879765-65879774 chr14:65879385-65879397
35	BHLHE40	chr14:65878424-65879949	GM12878	blood:	n/a	chr14:65879506-65879522 chr14:65879455-65879471
36	POLR2A	chr14:65878234-65879856	HEK293	kidney:	n/a	n/a
37	YY1	chr14:65878460-65878870	GM12878	blood:	n/a	chr14:65878601-65878615
38	GATA3	chr14:65878292-65879549	A549	lung:	n/a	n/a
39	HA-E2F1	chr14:65878271-65880300	MCF-7	breast:	n/a	chr14:65880135-65880144 chr14:65879719-65879730 chr14:65879587-65879596 chr14:65878601-65878610 chr14:65879340-65879352 chr14:65879395-65879404 chr14:65878511-65878520 chr14:65879655-65879669 chr14:65879340-65879349 chr14:65880263-65880272 chr14:65879514-65879523 chr14:65879763-65879773
40	POLR2A	chr14:65878265-65879565	GM12878	blood:	n/a	n/a
41	ZNF263	chr14:65878418-65879293	K562	blood:	n/a	n/a
42	POLR2A	chr14:65878482-65878876	K562	blood:	n/a	n/a
43	GABPA	chr14:65878086-65879510	MCF-7	breast:	n/a	chr14:65879340-65879349 chr14:65879391-65879405 chr14:65878680-65878689 chr14:65879394-65879408 chr14:65879394-65879405 chr14:65879396-65879405 chr14:65879482-65879491 chr14:65879394-65879403
44	PBX3	chr14:65878251-65878914	SK-N-SH	brain:	n/a	chr14:65878510-65878519 chr14:65878514-65878534 chr14:65878551-65878560
45	POLR2A	chr14:65878150-65879981	IMR90	lung:	n/a	n/a
46	PML	chr14:65878218-65880124	MCF-7	breast:	n/a	n/a
47	ELF1	chr14:65878223-65879983	GM12878	blood:	n/a	chr14:65879763-65879775 chr14:65878779-65878788 chr14:65879765-65879774 chr14:65879385-65879397
48	RAD21	chr14:65878259-65879921	SK-N-SH_RA	brain:	n/a	chr14:65879378-65879390 chr14:65879191-65879210
49	MAX	chr14:65878547-65879914	HepG2	liver:	n/a	chr14:65879334-65879344
50	NR2F2	chr14:65878185-65880635	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:65700230..65702841-chr14:65877569..65880268,3	MCF-7	breast:
2	chr14:65700105..65703075-chr14:65877781..65880441,2	MCF-7	breast:
3	chr14:65685385..65700060-chr14:65874568..65884730,76	MCF-7	breast:
4	chr14:65745595..65748280-chr14:65878483..65880878,2	MCF-7	breast:
5	chr14:65569137..65571197-chr14:65878383..65880649,2	MCF-7	breast:
6	chr14:65688460..65689522-chr14:65878564..65879464,3	MCF-7	breast:
7	chr14:65799114..65802639-chr14:65877920..65880470,4	MCF-7	breast:
8	chr14:65877301..65879579-chr20:36761978..36764479,2	MCF-7	breast:
9	chr14:65877799..65879344-chr20:52823519..52825312,2	MCF-7	breast:
10	chr14:65769045..65770910-chr14:65878599..65880667,2	MCF-7	breast:
11	chr14:65688822..65689388-chr14:65878671..65879347,2	MCF-7	breast:
12	chr14:65682951..65699539-chr14:65874873..65882779,51	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAX-11	chr14:65877311-65879335	NONHSAT037389

Variant related genes	Relation type
FUT8	TF binding region
ENSG00000266740	Chromatin interaction
ENSG00000259078	Chromatin interaction
ENSG00000101132	Chromatin interaction
ENSG00000258760	Chromatin interaction
ENSG00000255002	Chromatin interaction
ENSG00000125952	Chromatin interaction
ENSG00000258878	Chromatin interaction
ENSG00000198959	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10138570	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs10483780	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11158592	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11158593	0.93[CEU][hapmap];0.80[MEX][hapmap];0.80[EUR][1000 genomes]
rs11158596	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11158601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11158602	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11620749	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11621680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11622014	0.81[EUR][1000 genomes]
rs11627084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11628196	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11851576	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12589698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12879202	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12879971	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12882269	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12883815	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12887134	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12889002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12890123	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12890978	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12892058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12895074	0.88[EUR][1000 genomes]
rs1815654	0.87[ASN][1000 genomes]
rs1958561	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2002692	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2149841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2184603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2411816	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2411822	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783709	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3825640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4456409	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4581615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4899179	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902400	0.88[EUR][1000 genomes]
rs67071794	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7146742	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7152441	0.81[AFR][1000 genomes]
rs7153297	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7155541	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7161123	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs743085	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap]
rs867972	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs883081	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs883082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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	nsv832818	chr14:65706859-65882320	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv510639	chr14:65853883-65884315	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv3404983	chr14:65878424-65881572	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1953416	VTI1B	cis	parietal	SCAN
rs1953416	FUT8	cis	cerebellum	SCAN
rs1953416	HIF1A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65877600-65882200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:65877600-65885400	Active TSS	GM12878-XiMat	blood
3	chr14:65877800-65879000	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr14:65877800-65880400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:65877800-65880600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:65877800-65880600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:65877800-65881000	Active TSS	Fetal Intestine Small	intestine
8	chr14:65877800-65881600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr14:65877800-65882600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr14:65878000-65879000	Active TSS	Brain Germinal Matrix	brain
11	chr14:65878000-65879200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr14:65878000-65879800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr14:65878000-65879800	Active TSS	Colonic Mucosa	Colon
14	chr14:65878000-65880200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:65878000-65880200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr14:65878000-65880200	Active TSS	Stomach Smooth Muscle	stomach
17	chr14:65878000-65880400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr14:65878000-65880400	Active TSS	Fetal Lung	lung
19	chr14:65878000-65880400	Active TSS	Fetal Stomach	stomach
20	chr14:65878000-65880400	Active TSS	Rectal Smooth Muscle	rectum
21	chr14:65878000-65880400	Active TSS	Thymus	Thymus
22	chr14:65878000-65880400	Active TSS	HSMM	muscle
23	chr14:65878000-65880600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr14:65878000-65880600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr14:65878000-65880600	Active TSS	Fetal Brain Male	brain
26	chr14:65878000-65880600	Active TSS	Fetal Brain Female	brain
27	chr14:65878000-65880600	Active TSS	Small Intestine	intestine
28	chr14:65878000-65880600	Active TSS	NHLF	lung
29	chr14:65878000-65880800	Active TSS	Placenta	Placenta
30	chr14:65878000-65880800	Active TSS	Right Atrium	heart
31	chr14:65878000-65881000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr14:65878000-65881000	Active TSS	Fetal Kidney	kidney
33	chr14:65878000-65881000	Active TSS	HSMMtube	muscle
34	chr14:65878000-65881200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr14:65878000-65881400	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr14:65878000-65881800	Active TSS	Brain Angular Gyrus	brain
37	chr14:65878000-65881800	Active TSS	Fetal Intestine Large	intestine
38	chr14:65878000-65882400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:65878200-65879000	Active TSS	Fetal Heart	heart
40	chr14:65878200-65880200	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr14:65878200-65880200	Active TSS	Primary T cells from cord blood	blood
42	chr14:65878200-65880200	Active TSS	Primary T cells fromperipheralblood	blood
43	chr14:65878200-65880200	Active TSS	Fetal Muscle Leg	muscle
44	chr14:65878200-65880200	Active TSS	Fetal Thymus	thymus
45	chr14:65878200-65880200	Active TSS	Left Ventricle	heart
46	chr14:65878200-65880200	Active TSS	Pancreas	Pancrea
47	chr14:65878200-65880200	Active TSS	Right Ventricle	heart
48	chr14:65878200-65880400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr14:65878200-65880400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr14:65878200-65880400	Active TSS	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links