Variant report

Variant	rs6512238
Chromosome Location	chr19:18060457-18060458
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr19:18059974-18061771	GM12878	blood:	n/a	chr19:18060647-18060657 chr19:18061586-18061595 chr19:18060646-18060657 chr19:18061586-18061595

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18058883..18061817-chr19:18083400..18086380,2	K562	blood:
2	chr19:18058855..18062679-chr19:18075387..18079032,3	MCF-7	breast:
3	chr19:18059749..18060616-chr19:18107405..18108095,3	MCF-7	breast:
4	chr19:18055988..18065489-chr19:18073307..18083163,16	K562	blood:
5	chr19:18060053..18061688-chr19:18218502..18220719,2	K562	blood:
6	chr19:18057399..18062095-chr19:18108081..18112546,5	K562	blood:
7	chr19:18058787..18061046-chr19:18077855..18080971,5	K562	blood:
8	chr19:18058858..18061007-chr19:18390720..18393623,2	K562	blood:
9	chr19:17974807..17978167-chr19:18058036..18060976,4	K562	blood:
10	chr19:18059452..18062098-chr19:18102180..18104149,2	MCF-7	breast:
11	chr19:17969435..17972591-chr19:18056494..18062279,6	K562	blood:
12	chr19:17970109..17972099-chr19:18059372..18061707,2	MCF-7	breast:

No data

Variant related genes	Relation type
KCNN1	TF binding region
ENSG00000252591	Chromatin interaction
ENSG00000105643	Chromatin interaction
ENSG00000105642	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000105640	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1076356	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4808105	0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[ASN][1000 genomes]
rs6512237	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250332	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256003	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8099927	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8101684	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110033	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911214	chr19:17827442-18123965	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv833772	chr19:17965173-18139337	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv911226	chr19:18007077-18075077	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911227	chr19:18007077-18117646	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	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
8	nsv911228	chr19:18038782-18101830	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv911229	chr19:18042945-18117646	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	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
11	esv3406796	chr19:18057477-18060725	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	esv3358201	chr19:18058077-18060550	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv911230	chr19:18059744-18092442	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv911231	chr19:18059744-18095251	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18058600-18060800	Weak transcription	Gastric	stomach
2	chr19:18058600-18061000	Enhancers	K562	blood
3	chr19:18059200-18060800	Weak transcription	Lung	lung
4	chr19:18059200-18062200	Enhancers	Fetal Brain Male	brain
5	chr19:18059200-18063800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
6	chr19:18059200-18064400	Enhancers	Pancreas	Pancrea
7	chr19:18059400-18060800	Enhancers	Brain Substantia Nigra	brain
8	chr19:18059400-18062800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:18059400-18062800	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr19:18059400-18064600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:18059600-18060600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
12	chr19:18059600-18061400	Bivalent Enhancer	Fetal Intestine Small	intestine
13	chr19:18059600-18061600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr19:18059600-18061800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:18059600-18062200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:18059600-18064000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr19:18059600-18064200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
18	chr19:18059800-18060600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:18059800-18060600	Bivalent Enhancer	Brain Hippocampus Middle	brain
20	chr19:18059800-18060800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:18059800-18060800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:18059800-18060800	Weak transcription	Right Atrium	heart
23	chr19:18059800-18060800	Bivalent Enhancer	NHEK	skin
24	chr19:18059800-18061200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:18059800-18061200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr19:18059800-18061200	Weak transcription	Fetal Kidney	kidney
27	chr19:18059800-18061400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr19:18059800-18061400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:18059800-18061400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:18059800-18061800	Bivalent Enhancer	NH-A	brain
31	chr19:18059800-18063200	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr19:18059800-18063600	Bivalent Enhancer	Fetal Intestine Large	intestine
33	chr19:18059800-18063800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
34	chr19:18059800-18064000	Bivalent Enhancer	Fetal Thymus	thymus
35	chr19:18059800-18064200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr19:18059800-18064400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr19:18060000-18060600	Bivalent Enhancer	Spleen	Spleen
38	chr19:18060000-18060800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:18060000-18060800	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr19:18060000-18060800	Weak transcription	A549	lung
41	chr19:18060000-18061000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr19:18060000-18061000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:18060000-18061000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
44	chr19:18060000-18061000	Enhancers	Left Ventricle	heart
45	chr19:18060000-18061200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:18060000-18061200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
47	chr19:18060000-18061200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
48	chr19:18060000-18061200	Bivalent Enhancer	Fetal Stomach	stomach
49	chr19:18060000-18061400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:18060000-18061400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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