Variant report

Variant	rs11668601
Chromosome Location	chr19:18214521-18214522
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	RFX5	chr19:18213633-18216347	IMR90	lung:	n/a	chr19:18215372-18215381 chr19:18215368-18215383 chr19:18215369-18215383 chr19:18215371-18215386 chr19:18215371-18215386
2	RFX5	chr19:18213577-18217211	SK-N-SH	brain:	n/a	chr19:18215372-18215381 chr19:18215368-18215383 chr19:18215369-18215383 chr19:18215371-18215386 chr19:18215371-18215386
3	RFX5	chr19:18214506-18214588	H1-hESC	embryonic stem cell:	n/a	n/a
4	RFX5	chr19:18214494-18214689	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18207064..18208834-chr19:18213992..18216646,2	MCF-7	breast:
2	chr19:18213855..18215840-chr19:18226802..18229759,2	K562	blood:
3	chr19:18214304..18215890-chr19:18263415..18265130,2	K562	blood:
4	chr19:18052659..18054243-chr19:18211950..18214668,2	K562	blood:
5	chr19:18214257..18217360-chr19:18228399..18230348,3	MCF-7	breast:
6	chr19:18212286..18215069-chr19:18221126..18224068,2	K562	blood:
7	chr19:18201667..18204008-chr19:18212882..18215554,2	MCF-7	breast:
8	chr19:18185895..18188337-chr19:18214059..18216560,2	K562	blood:
9	chr19:18208517..18210174-chr19:18213137..18216099,2	K562	blood:

Variant related genes	Relation type
IL12RB1	TF binding region
ENSG00000099308	Chromatin interaction
ENSG00000105647	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000096996	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11666281	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11666424	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666906	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs273488	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs273492	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs273507	1.00[ASN][1000 genomes]
rs273510	1.00[ASN][1000 genomes]
rs4808114	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808115	0.90[ASN][1000 genomes]
rs4808745	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808751	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56252442	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56345159	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60146811	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66464318	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67234314	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72999447	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72999466	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs885683	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18209400-18214600	Weak transcription	A549	lung
2	chr19:18209400-18215000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:18209600-18215000	Weak transcription	Hela-S3	cervix
4	chr19:18210000-18215400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:18210200-18215000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:18210200-18215000	Weak transcription	Ovary	ovary
7	chr19:18210200-18215000	Weak transcription	Right Atrium	heart
8	chr19:18210200-18215000	Weak transcription	HMEC	breast
9	chr19:18210400-18215000	Weak transcription	Pancreas	Pancrea
10	chr19:18210600-18214600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:18210600-18215200	Weak transcription	Lung	lung
12	chr19:18210800-18214600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:18210800-18214800	Weak transcription	Colonic Mucosa	Colon
14	chr19:18210800-18215000	Weak transcription	Primary T cells from cord blood	blood
15	chr19:18210800-18215000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:18210800-18215000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:18210800-18215000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:18210800-18215000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:18210800-18215000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:18210800-18215000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:18210800-18215000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr19:18210800-18215000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:18210800-18215200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:18211000-18214600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:18211000-18214600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:18211600-18214600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr19:18211800-18215200	Weak transcription	Gastric	stomach
28	chr19:18212000-18214800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:18212000-18215000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:18212000-18215000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:18212000-18215000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:18212200-18215000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:18212200-18215000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:18212200-18215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:18212200-18215000	Weak transcription	Brain Angular Gyrus	brain
36	chr19:18212200-18215000	Weak transcription	Brain Anterior Caudate	brain
37	chr19:18212400-18214600	Weak transcription	Liver	Liver
38	chr19:18212400-18215000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:18212400-18215000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:18212400-18215000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:18212400-18215000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:18212400-18215000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:18212400-18215000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:18212400-18215200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:18212400-18215400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:18212600-18215000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:18212600-18215000	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:18212600-18215200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:18213600-18214600	Weak transcription	Small Intestine	intestine
50	chr19:18213600-18215000	Enhancers	Brain Substantia Nigra	brain

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