Variant report

Variant	rs2238654
Chromosome Location	chr19:18962061-18962062
allele	A/G
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	STAT3	chr19:18961944-18962075	MCF10A-Er-Src	breast:	n/a	chr19:18961954-18961966
2	POLR2A	chr19:18961152-18963785	K562	blood:	n/a	n/a
3	POLR2A	chr19:18961341-18962243	GM12892	blood:	n/a	n/a
4	MXI1	chr19:18961105-18962088	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:18961928-18962114	GM12878	blood:	n/a	n/a
6	GATA2	chr19:18962046-18962481	HUVEC	blood vessel:	n/a	chr19:18962070-18962077
7	POLR2A	chr19:18961837-18962220	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18943201..18946442-chr19:18960453..18965147,6	MCF-7	breast:
2	chr19:18960784..18962475-chr19:18978438..18980131,2	K562	blood:
3	chr19:18960692..18962403-chr19:18990602..18992305,2	K562	blood:

Variant related genes	Relation type
UPF1	TF binding region
ENSG00000005007	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2238653	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2238656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238657	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808861	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808863	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59045002	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh 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	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911299	chr19:18939954-18984843	Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18951800-18977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:18953200-18977600	Weak transcription	Fetal Heart	heart
3	chr19:18954800-18979800	Strong transcription	Dnd41	blood
4	chr19:18955400-18963800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:18955600-18966600	Genic enhancers	Fetal Muscle Leg	muscle
6	chr19:18956200-18978400	Strong transcription	Thymus	Thymus
7	chr19:18956600-18962200	Genic enhancers	NHEK	skin
8	chr19:18956600-18972000	Genic enhancers	Fetal Muscle Trunk	muscle
9	chr19:18956800-18966800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:18956800-18975200	Strong transcription	HepG2	liver
11	chr19:18957800-18962200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr19:18957800-18962200	Enhancers	Ovary	ovary
13	chr19:18958200-18964600	Genic enhancers	Fetal Thymus	thymus
14	chr19:18958200-18966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:18958200-18977000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:18958400-18962600	Strong transcription	Hela-S3	cervix
17	chr19:18958400-18964200	Genic enhancers	Placenta	Placenta
18	chr19:18958400-18964400	Strong transcription	A549	lung
19	chr19:18958400-18977600	Strong transcription	Fetal Intestine Large	intestine
20	chr19:18958400-18979000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:18958400-18979200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr19:18958400-18979400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:18958400-18979400	Strong transcription	Primary T cells from cord blood	blood
24	chr19:18958400-18979400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:18958400-18980200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:18958600-18973200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:18958600-18976200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:18958600-18979000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:18958600-18979200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:18958600-18979400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:18958600-18979600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:18958800-18964600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:18958800-18979200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr19:18958800-18979200	Strong transcription	Brain Germinal Matrix	brain
35	chr19:18959000-18962200	Genic enhancers	Colonic Mucosa	Colon
36	chr19:18959000-18962200	Genic enhancers	Lung	lung
37	chr19:18959000-18962200	Enhancers	Right Atrium	heart
38	chr19:18959000-18962600	Genic enhancers	Right Ventricle	heart
39	chr19:18959000-18963000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:18959000-18979000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:18959000-18979000	Strong transcription	Gastric	stomach
42	chr19:18959200-18963400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:18959200-18979200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr19:18959800-18964200	Weak transcription	Fetal Brain Male	brain
45	chr19:18959800-18978800	Strong transcription	Fetal Brain Female	brain
46	chr19:18960000-18962200	Genic enhancers	Colon Smooth Muscle	Colon
47	chr19:18960000-18963800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:18960000-18979400	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:18960200-18965000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr19:18960400-18962200	Genic enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links