Variant report

Variant	rs16975619
Chromosome Location	chr19:42392441-42392442
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	POLR2A	chr19:42390762-42392615	GM12892	blood:	n/a	n/a
2	EGR1	chr19:42391497-42392509	HCT-116	colon:	n/a	chr19:42391923-42391936 chr19:42391641-42391650 chr19:42391951-42391965 chr19:42392012-42392026 chr19:42391918-42391940
3	POLR2A	chr19:42390925-42392449	GM12878	blood:	n/a	n/a
4	EGR1	chr19:42391568-42392545	HCT-116	colon:	n/a	chr19:42391923-42391936 chr19:42391641-42391650 chr19:42391951-42391965 chr19:42392012-42392026 chr19:42391918-42391940
5	POLR2A	chr19:42389937-42394570	GM12878	blood:	n/a	n/a
6	FOXA2	chr19:42391540-42392508	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:42391930-42392514	K562	blood:	n/a	n/a
8	POLR2A	chr19:42390846-42392476	GM12892	blood:	n/a	n/a
9	MTA3	chr19:42390605-42392477	GM12878	blood:	n/a	n/a
10	SIN3AK20	chr19:42391653-42392571	MCF-7	breast:	n/a	n/a
11	POLR2A	chr19:42390874-42392486	GM12878	blood:	n/a	n/a
12	HDAC2	chr19:42391881-42392460	MCF-7	breast:	n/a	chr19:42392037-42392046
13	POLR2A	chr19:42392351-42392602	HepG2	liver:	n/a	n/a
14	TBL1XR1	chr19:42390983-42392466	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:42390651-42392446	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:42389706-42394346	SK-N-MC	brain:	n/a	n/a
17	EBF1	chr19:42390852-42392521	GM12878	blood:	n/a	chr19:42391517-42391526 chr19:42391515-42391528 chr19:42391516-42391527
18	POLR2A	chr19:42390934-42392571	GM12878	blood:	n/a	n/a
19	HDAC2	chr19:42391769-42392470	MCF-7	breast:	n/a	chr19:42392037-42392046
20	ELF1	chr19:42391084-42392495	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:42390528..42393391-chr19:42425919..42428755,3	MCF-7	breast:
2	chr19:42392091..42393958-chr19:42398936..42401032,2	MCF-7	breast:
3	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
4	chr19:42390140..42393678-chr19:42394261..42398306,6	K562	blood:
5	chr19:42391577..42392478-chr19:42455568..42456267,3	MCF-7	breast:
6	chr19:42390499..42394130-chr19:42395488..42398499,5	MCF-7	breast:
7	chr19:42392209..42393764-chr19:42436323..42438762,2	MCF-7	breast:
8	chr19:42391492..42392504-chr19:42461709..42462601,3	MCF-7	breast:
9	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
10	chr19:42390553..42393119-chr19:42395224..42396776,2	MCF-7	breast:
11	chr19:42391908..42392858-chr19:42455448..42456435,2	K562	blood:
12	chr19:42390344..42392993-chr19:42439270..42441134,2	MCF-7	breast:
13	chr19:42385266..42389164-chr19:42392215..42397025,5	MCF-7	breast:
14	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
15	chr19:42392300..42393961-chr19:42403075..42405096,2	K562	blood:
16	chr19:42390993..42392677-chr19:42461992..42463492,2	K562	blood:
17	chr19:42390448..42392513-chr19:42434205..42436040,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000105404	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10401189	0.91[ASN][1000 genomes]
rs10401937	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10402667	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10403081	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10417495	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419314	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11878536	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11878555	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12104228	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2288509	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288510	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288511	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288512	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2303798	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28396197	0.93[AMR][1000 genomes]
rs28521795	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28706300	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3745222	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6509003	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs717225	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252790	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7252800	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253691	0.94[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73550603	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73550610	0.87[ASN][1000 genomes]
rs73550618	0.83[EUR][1000 genomes]
rs8109784	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109959	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110305	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113339	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113686	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs891169	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs891170	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs891171	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs891172	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389000-42396000	Weak transcription	Aorta	Aorta
2	chr19:42389000-42396000	Weak transcription	Ovary	ovary
3	chr19:42389200-42392600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
4	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
5	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
6	chr19:42389400-42392600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr19:42389400-42392800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr19:42389400-42393000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:42389400-42393600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:42389400-42398200	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:42389400-42402000	Weak transcription	Psoas Muscle	Psoas
12	chr19:42389400-42406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
14	chr19:42389800-42392800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:42389800-42393000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:42389800-42409000	Strong transcription	Fetal Stomach	stomach
17	chr19:42390000-42392600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:42390200-42392800	Enhancers	NH-A	brain
19	chr19:42390400-42392600	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr19:42390400-42392600	Active TSS	Thymus	Thymus
21	chr19:42390400-42392800	Enhancers	Brain Angular Gyrus	brain
22	chr19:42390600-42393200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:42390800-42392600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr19:42390800-42411200	Weak transcription	Hela-S3	cervix
25	chr19:42391000-42392600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr19:42391000-42392600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:42391000-42392600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr19:42391000-42392600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr19:42391000-42392600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:42391000-42392600	Genic enhancers	Placenta	Placenta
31	chr19:42391000-42392800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:42391000-42393000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:42391000-42394000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
34	chr19:42391200-42392600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr19:42391200-42393200	Weak transcription	HSMMtube	muscle
36	chr19:42391200-42393800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:42391400-42393200	Weak transcription	NHDF-Ad	bronchial
38	chr19:42391400-42396800	Weak transcription	Brain Anterior Caudate	brain
39	chr19:42391400-42407400	Weak transcription	K562	blood
40	chr19:42391600-42392600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr19:42391600-42392600	Weak transcription	Left Ventricle	heart
42	chr19:42391600-42392600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:42391600-42393400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:42391600-42396000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:42391600-42399600	Weak transcription	HUVEC	blood vessel
46	chr19:42391600-42404600	Weak transcription	HSMM	muscle
47	chr19:42391800-42392600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:42391800-42392600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr19:42391800-42392600	Weak transcription	Adipose Nuclei	Adipose
50	chr19:42391800-42393000	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links