Variant report

Variant	rs16975789
Chromosome Location	chr19:42960362-42960363
allele	C/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	JUND	chr19:42959674-42960399	HCT-116	colon:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
2	JUND	chr19:42959670-42960409	HCT-116	colon:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
3	FOSL2	chr19:42959768-42960382	A549	lung:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960039-42960050 chr19:42960025-42960033 chr19:42960022-42960033
4	FOSL1	chr19:42959604-42960394	HCT-116	colon:	n/a	chr19:42960036-42960047 chr19:42960023-42960035 chr19:42960025-42960033
5	FOXA2	chr19:42959715-42960368	A549	lung:	n/a	n/a
6	SP1	chr19:42959667-42960451	HCT-116	colon:	n/a	chr19:42959895-42959905
7	CBX3	chr19:42959757-42960403	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42947132..42948888-chr19:42958718..42960967,2	MCF-7	breast:

Variant related genes	Relation type
LIPE-AS1	TF binding region
ENSG00000189377	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10084159	0.96[ASN][1000 genomes]
rs10401271	0.97[ASN][1000 genomes]
rs10402401	0.82[MEX][hapmap]
rs10403517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405445	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10405906	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10413014	0.82[MEX][hapmap]
rs10413413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10416089	0.84[EUR][1000 genomes]
rs10422987	0.93[EUR][1000 genomes]
rs10469284	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10469285	0.97[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs11665870	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11665935	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666350	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11668460	0.81[AMR][1000 genomes]
rs11668599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11671272	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11671846	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11673645	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11879306	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11881517	0.93[EUR][1000 genomes]
rs11882150	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12611218	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13343936	0.97[ASN][1000 genomes]
rs16975865	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16975890	0.88[YRI][hapmap];0.83[AMR][1000 genomes]
rs28411988	0.93[EUR][1000 genomes]
rs4080606	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55850134	0.85[EUR][1000 genomes]
rs60313903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7253056	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8102439	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs8103891	0.93[EUR][1000 genomes]
rs8106570	0.90[EUR][1000 genomes]
rs8107254	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107790	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8112156	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs851298	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs851301	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs851302	0.90[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	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS 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 miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42952400-42964400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:42954400-42961000	Enhancers	Primary B cells from cord blood	blood
3	chr19:42954600-42961600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:42955400-42964000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:42955400-42964600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:42955800-42966400	Weak transcription	GM12878-XiMat	blood
7	chr19:42957000-42961400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:42957000-42961400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:42957000-42966000	Weak transcription	Left Ventricle	heart
10	chr19:42957400-42964600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:42957400-42970600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:42958200-42960400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr19:42959000-42960400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr19:42959000-42960400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr19:42959000-42960400	Enhancers	Fetal Intestine Large	intestine
16	chr19:42959000-42960600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:42959000-42960600	Enhancers	Duodenum Mucosa	Duodenum
18	chr19:42959000-42961600	Enhancers	Fetal Intestine Small	intestine
19	chr19:42959200-42960400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr19:42959200-42960400	Enhancers	Stomach Mucosa	stomach
21	chr19:42959200-42960600	Enhancers	HMEC	breast
22	chr19:42959200-42961000	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr19:42959400-42960400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:42959400-42960400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:42959400-42960400	Enhancers	HepG2	liver
26	chr19:42959400-42960400	Enhancers	NHEK	skin
27	chr19:42959400-42960800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr19:42959600-42960400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr19:42959800-42960400	Enhancers	Primary B cells from peripheral blood	blood
30	chr19:42959800-42960400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:42959800-42960400	Enhancers	Adipose Nuclei	Adipose
32	chr19:42959800-42960400	Enhancers	Right Atrium	heart
33	chr19:42960000-42960400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr19:42960000-42960400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:42960000-42960400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr19:42960000-42960400	Enhancers	Esophagus	oesophagus
37	chr19:42960000-42961400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:42960000-42964600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:42960000-42970200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:42960200-42960400	Enhancers	A549	lung
41	chr19:42960200-42960800	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr19:42960200-42963200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:42960200-42963400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:42960200-42964600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr19:42960200-42970000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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