Variant report

Variant	rs397319
Chromosome Location	chr5:14405761-14405762
allele	A/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	MXI1	chr5:14405352-14407509	IMR90	lung:	n/a	chr5:14405924-14405939
2	POLR2A	chr5:14405212-14405825	PANC-1	pancreas:	n/a	n/a
3	JUND	chr5:14405705-14408375	SK-N-SH	brain:	n/a	chr5:14407724-14407738 chr5:14405848-14405860
4	TCF12	chr5:14405496-14407266	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr5:14405233-14406108	HUVEC	blood vessel:	n/a	n/a
6	MAZ	chr5:14405448-14407773	IMR90	lung:	n/a	chr5:14406138-14406148
7	CTCF	chr5:14405410-14405793	K562	blood:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599
8	ZNF143	chr5:14405433-14405778	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:14405526-14405800	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr5:14405595-14405854	GM12878	blood:	n/a	n/a
11	RAD21	chr5:14405391-14405860	HCT-116	colon:	n/a	chr5:14405491-14405505
12	CTCF	chr5:14405660-14405810	HFF-Myc	foreskin:	n/a	n/a
13	RAD21	chr5:14405067-14405993	SK-N-SH	brain:	n/a	chr5:14405491-14405505
14	CTCF	chr5:14405680-14405830	HAc	cerebellar:	n/a	n/a
15	RAD21	chr5:14405380-14405768	ECC-1	luminal epithelium:	n/a	chr5:14405491-14405505
16	CTCF	chr5:14405324-14405832	HCT-116	colon:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599
17	CTCF	chr5:14405409-14405851	MCF-7	breast:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599
18	CTCF	chr5:14405199-14406264	SK-N-SH	brain:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599
19	CTCF	chr5:14405302-14405795	MCF-7	breast:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599
20	CTCF	chr5:14405293-14405766	K562	blood:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599
21	CTCF	chr5:14405720-14405870	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:14405747-14405797	A549	lung:	n/a
2	chr5:14405747-14405797	HL-60	blood:	n/a
3	chr5:14405747-14405797	SAEC	small airway:	n/a
4	chr5:14405747-14405797	HepG2	liver:	n/a
5	chr5:14405747-14405797	HCT-116	colon:	n/a
6	chr5:14405747-14405797	GM19239	blood:	n/a
7	chr5:14405747-14405797	HIPEpiC	eye:	n/a
8	chr5:14405747-14405797	SK-N-SH_RA	brain:	n/a
9	chr5:14405747-14405797	HEEpiC	esophagus:	n/a
10	chr5:14405747-14405797	HRPEpiC	eye:	n/a
11	chr5:14405747-14405797	PFSK-1	brain:	n/a
12	chr5:14405747-14405797	AG04450	lung:	fetal
13	chr5:14405747-14405797	CMK	blood:	n/a
14	chr5:14405747-14405797	NH-A	brain:	n/a
15	chr5:14405747-14405797	SK-N-MC	brain:	n/a
16	chr5:14405747-14405797	SKMC	muscle:	n/a
17	chr5:14405747-14405797	MCF10A-Er-Src	breast:	n/a
18	chr5:14405747-14405797	PrEC	prostate:	n/a
19	chr5:14405747-14405797	HEK293	kidney:	embryo
20	chr5:14405747-14405797	K562	blood:	n/a
21	chr5:14405747-14405797	RPTEC	kidney:	n/a
22	chr5:14405747-14405797	LNCaP	prostate:	n/a
23	chr5:14405747-14405797	AG09309	skin:	n/a
24	chr5:14405747-14405797	Jurkat	blood:	n/a
25	chr5:14405747-14405797	ovcar-3	ovarian:	n/a
26	chr5:14405747-14405797	IMR90	lung:	fetal
27	chr5:14405747-14405797	Hepatocyte	liver:	n/a
28	chr5:14405747-14405797	AG09319	gingival:	n/a
29	chr5:14405747-14405797	HUVEC	blood vessel:	n/a
30	chr5:14405747-14405797	T-47D	breast:	n/a
31	chr5:14405747-14405797	HRCEpiC	kidney:	n/a
32	chr5:14405747-14405797	U87	brain:	n/a
33	chr5:14405747-14405797	NHBE	bronchial:	n/a
34	chr5:14405747-14405797	NT2-D1	testis:	n/a
35	chr5:14405747-14405797	GM06990	blood:	n/a
36	chr5:14405747-14405797	ECC-1	luminal epithelium:	n/a
37	chr5:14405747-14405797	AG10803	skin:	n/a
38	chr5:14405747-14405797	Hela-S3	cervix:	n/a
39	chr5:14405747-14405797	Caco-2	colon:	n/a
40	chr5:14405747-14405797	GM12892	blood:	n/a
41	chr5:14405747-14405797	AoSMC	blood vessel:	n/a
42	chr5:14405747-14405797	HNPCEpiC	eye:	n/a
43	chr5:14405747-14405797	NHDF-neo	bronchial:	n/a
44	chr5:14405747-14405797	HRE	kidney:	n/a
45	chr5:14405747-14405797	HAEpiC	amniotic membrane:	n/a
46	chr5:14405747-14405797	MCF-7	breast:	n/a
47	chr5:14405747-14405797	HMEC	breast:	n/a
48	chr5:14405747-14405797	ProgFib	skin:	n/a
49	chr5:14405747-14405797	BE2_C	brain:	n/a
50	chr5:14405747-14405797	HPAEpiC	pulmonary alveolar:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14405228..14405866-chr5:14648409..14649049,2	MCF-7	breast:

Variant related genes	Relation type
TRIO	TF binding region
TRIO	CpG island

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11955578	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11957060	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11957857	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13172149	0.80[EUR][1000 genomes]
rs13172877	0.80[EUR][1000 genomes]
rs13189406	0.80[EUR][1000 genomes]
rs13356126	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs154151	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs173947	0.96[ASN][1000 genomes]
rs185355	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs187190	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs187667	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247136	0.94[ASN][1000 genomes]
rs247137	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs256412	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256418	0.83[ASN][1000 genomes]
rs28343	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30606	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs30607	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs30608	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs30609	0.92[ASN][1000 genomes]
rs30610	0.90[ASN][1000 genomes]
rs30611	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs30766	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30767	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30768	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30772	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs30785	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30786	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30787	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs30788	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30789	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs30790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30793	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs30794	1.00[JPT][hapmap]
rs30795	1.00[JPT][hapmap]
rs30799	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs30800	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30801	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs378369	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs382403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389729	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40278	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42206	0.96[ASN][1000 genomes]
rs42404	0.89[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs42555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs434279	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4702029	0.89[CEU][hapmap]

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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
2	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:14387200-14405800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:14388800-14407200	Weak transcription	Small Intestine	intestine
6	chr5:14392200-14406600	Weak transcription	Primary T cells from cord blood	blood
7	chr5:14392400-14406000	Weak transcription	Fetal Heart	heart
8	chr5:14392400-14426800	Weak transcription	Psoas Muscle	Psoas
9	chr5:14393600-14413600	Strong transcription	Primary B cells from cord blood	blood
10	chr5:14395200-14406600	Weak transcription	Fetal Kidney	kidney
11	chr5:14395800-14406000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr5:14395800-14406000	Weak transcription	Brain Substantia Nigra	brain
13	chr5:14397600-14406200	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:14398200-14406000	Weak transcription	Thymus	Thymus
15	chr5:14398400-14406000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:14398600-14406000	Weak transcription	Esophagus	oesophagus
17	chr5:14398800-14406200	Weak transcription	Aorta	Aorta
18	chr5:14399000-14419800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:14399600-14416400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr5:14400200-14413400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:14400400-14406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:14400600-14415000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:14400800-14408600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:14400800-14416000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:14401000-14406600	Weak transcription	Left Ventricle	heart
26	chr5:14401200-14406200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:14401200-14407400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:14401400-14405800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:14401400-14406200	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:14401400-14406600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:14401600-14406000	Weak transcription	Colonic Mucosa	Colon
32	chr5:14401600-14407400	Strong transcription	Fetal Muscle Leg	muscle
33	chr5:14401800-14405800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:14401800-14407200	Weak transcription	Fetal Brain Male	brain
35	chr5:14402000-14406000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:14402000-14406000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:14402400-14405800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:14402600-14406400	Weak transcription	Hela-S3	cervix
39	chr5:14402600-14407200	Strong transcription	Fetal Stomach	stomach
40	chr5:14402600-14407600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:14403000-14405800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr5:14403200-14406000	Weak transcription	Fetal Lung	lung
43	chr5:14403200-14410000	Weak transcription	Brain Angular Gyrus	brain
44	chr5:14404000-14405800	Weak transcription	Fetal Thymus	thymus
45	chr5:14404000-14409400	Genic enhancers	HSMM	muscle
46	chr5:14404000-14420600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:14404200-14405800	Strong transcription	NHDF-Ad	bronchial
48	chr5:14404200-14406000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr5:14404200-14412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:14404400-14415000	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links