Variant report

Variant	rs41481544
Chromosome Location	chr19:18394079-18394080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:18385002-18394564	K562	blood:	n/a	n/a
2	POLR2A	chr19:18382160-18394577	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:18388726-18394103	HL-60	blood:	n/a	n/a
4	POLR2A	chr19:18384125-18394577	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:18388630-18394093	K562	blood:	n/a	n/a
6	POLR2A	chr19:18387352-18394088	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:18388708-18394079	H1-hESC	embryonic stem cell:	n/a	n/a
8	CHD1	chr19:18388700-18394109	IMR90	lung:	n/a	n/a
9	POLR2A	chr19:18379986-18394443	IMR90	lung:	n/a	n/a
10	SP1	chr19:18391689-18394135	HCT-116	colon:	n/a	chr19:18393795-18393809 chr19:18392536-18392545 chr19:18392534-18392545 chr19:18392534-18392546 chr19:18392535-18392544 chr19:18392535-18392545 chr19:18392534-18392546 chr19:18392536-18392545 chr19:18392535-18392545 chr19:18392998-18393008 chr19:18393332-18393346

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18311216..18316508-chr19:18389022..18394678,9	MCF-7	breast:
2	chr19:18385043..18394940-chr19:18518893..18533267,53	K562	blood:
3	chr19:18388423..18395098-chr19:18483334..18487110,13	K562	blood:
4	chr19:18388472..18395098-chr19:18481027..18487774,21	K562	blood:
5	chr19:18391038..18394210-chr19:18525828..18530797,8	MCF-7	breast:
6	chr19:18260692..18269532-chr19:18383927..18395911,19	K562	blood:
7	chr19:18387676..18394124-chr19:18495437..18503905,30	K562	blood:
8	chr19:18384108..18395354-chr19:18534355..18544725,18	K562	blood:
9	chr19:18382564..18395263-chr19:18409643..18446343,165	MCF-7	breast:
10	chr19:18392874..18395450-chr19:18668198..18669959,2	K562	blood:
11	chr19:18302314..18304675-chr19:18392994..18395243,2	MCF-7	breast:
12	chr19:18390025..18394312-chr19:18496571..18499733,6	MCF-7	breast:
13	chr19:18392266..18394628-chr19:18631659..18634590,3	K562	blood:
14	chr19:18387676..18394344-chr19:18495021..18501696,25	K562	blood:
15	chr19:18391626..18394860-chr19:18506004..18508591,3	K562	blood:
16	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
17	chr19:18301148..18305001-chr19:18389528..18394862,10	MCF-7	breast:
18	chr19:18390145..18394362-chr19:18451018..18457221,11	MCF-7	breast:

No data

Variant related genes	Relation type
JUND	TF binding region
ENSG00000130520	Chromatin interaction
ENSG00000175489	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000269145	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000130517	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000105649	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000268650	Chromatin interaction
ENSG00000254858	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000239821	Chromatin interaction
ENSG00000105647	Chromatin interaction
ENSG00000221167	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1079165	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1079166	0.92[ASN][1000 genomes]
rs10854164	0.96[ASN][1000 genomes]
rs12459276	0.82[EUR][1000 genomes]
rs12460547	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12461261	0.92[ASN][1000 genomes]
rs12461701	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12461751	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1421720	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1549143	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17711565	0.82[ASN][1000 genomes]
rs41347350	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808125	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808778	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57090641	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58555271	0.81[EUR][1000 genomes]
rs59961449	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60086589	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60170051	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62120437	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247237	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7247767	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7248070	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103549	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic 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	136 gene(s)	inside rSNPs	diseases
4	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
6	nsv911268	chr19:18351674-18395537	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
7	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
8	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
9	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
10	nsv828472	chr19:18377725-18404131	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
11	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
12	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
13	esv1793726	chr19:18381600-18400786	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	104 gene(s)	inside rSNPs	diseases
14	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
15	esv1801478	chr19:18391070-18395537	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41481544	KIAA1683	cis	Thyroid	GTEx
rs41481544	KIAA1683	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18393200-18394200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr19:18393200-18394400	Enhancers	Spleen	Spleen
3	chr19:18393400-18394600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:18393600-18394400	Enhancers	Primary B cells from peripheral blood	blood
5	chr19:18393600-18394400	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr19:18393600-18394400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:18393600-18394400	Enhancers	Fetal Thymus	thymus
8	chr19:18393600-18394400	Enhancers	Right Ventricle	heart
9	chr19:18393600-18394600	Enhancers	Placenta	Placenta
10	chr19:18393600-18394600	Enhancers	Left Ventricle	heart
11	chr19:18393600-18394600	Enhancers	Psoas Muscle	Psoas
12	chr19:18393600-18394800	Enhancers	Fetal Intestine Large	intestine
13	chr19:18393600-18394800	Enhancers	Fetal Intestine Small	intestine
14	chr19:18393600-18395600	Weak transcription	Small Intestine	intestine
15	chr19:18393800-18394200	Enhancers	Primary B cells from cord blood	blood
16	chr19:18393800-18394200	Enhancers	Fetal Heart	heart
17	chr19:18393800-18394400	Enhancers	Primary hematopoietic stem cells	blood
18	chr19:18393800-18394400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:18393800-18394400	Enhancers	Colonic Mucosa	Colon
20	chr19:18393800-18394400	Enhancers	Duodenum Mucosa	Duodenum
21	chr19:18393800-18394400	Enhancers	Fetal Muscle Trunk	muscle
22	chr19:18393800-18394400	Enhancers	Fetal Muscle Leg	muscle
23	chr19:18393800-18394400	Enhancers	Fetal Stomach	stomach
24	chr19:18393800-18394400	Enhancers	Pancreas	Pancrea
25	chr19:18393800-18394400	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr19:18393800-18394600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr19:18393800-18394600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr19:18393800-18394600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr19:18393800-18394600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:18393800-18394600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:18393800-18394600	Enhancers	Adipose Nuclei	Adipose
32	chr19:18393800-18394600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:18393800-18394600	Enhancers	K562	blood
34	chr19:18393800-18394800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr19:18393800-18394800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:18393800-18394800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr19:18393800-18394800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr19:18393800-18395600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr19:18393800-18395600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:18393800-18396400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:18393800-18396800	Weak transcription	Ovary	ovary
42	chr19:18393800-18397400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr19:18393800-18397400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr19:18393800-18397400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:18393800-18397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:18393800-18397400	Weak transcription	Esophagus	oesophagus
47	chr19:18393800-18397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:18393800-18397800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:18393800-18398000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr19:18393800-18398000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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