Variant report

Variant	rs11667176
Chromosome Location	chr19:18080208-18080209
allele	A/G
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:6)
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	POLR2A	chr19:18080184-18080313	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18074215..18077620-chr19:18078489..18082245,4	K562	blood:
2	chr19:18055988..18065489-chr19:18073307..18083163,16	K562	blood:
3	chr19:18079573..18082569-chr19:18112067..18113857,2	K562	blood:
4	chr19:18079287..18080876-chr19:18108150..18111999,3	K562	blood:
5	chr19:18080070..18081745-chr19:18084699..18086287,2	K562	blood:
6	chr19:18052887..18055484-chr19:18079172..18081041,3	K562	blood:

No data

Variant related genes	Relation type
RNA5SP468	TF binding region
ENSG00000105642	Chromatin interaction
ENSG00000105643	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2278991	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2278992	0.86[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2278993	0.86[GIH][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3746192	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808726	0.84[ASN][1000 genomes]
rs59538368	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6512239	0.84[ASN][1000 genomes]
rs6512241	0.88[ASN][1000 genomes]
rs6512242	0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6512243	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7254547	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73024616	0.83[ASN][1000 genomes]
rs8107891	0.83[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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv911232	chr19:18061509-18123965	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
13	nsv911233	chr19:18061639-18083619	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv911234	chr19:18075807-18128388	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11667176	KIAA0892	cis	cerebellum	SCAN
rs11667176	LSM4	cis	cerebellum	SCAN
rs11667176	JUND	cis	cerebellum	SCAN
rs11667176	ZNF714	cis	parietal	SCAN
rs11667176	CASP14	cis	cerebellum	SCAN
rs11667176	KIAA1683	cis	cerebellum	SCAN
rs11667176	CCDC124	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18078400-18111200	Weak transcription	Right Atrium	heart
2	chr19:18078600-18080600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:18078800-18080600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr19:18078800-18080600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr19:18078800-18080600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:18078800-18084400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:18078800-18085400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:18078800-18091800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:18078800-18093400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:18078800-18107600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:18079200-18080400	Enhancers	K562	blood
12	chr19:18079600-18080600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr19:18079600-18081600	Weak transcription	Fetal Brain Male	brain
14	chr19:18079600-18082600	Weak transcription	Brain Germinal Matrix	brain
15	chr19:18079600-18085200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:18079800-18084400	Weak transcription	Fetal Brain Female	brain
17	chr19:18080000-18085000	Weak transcription	Fetal Stomach	stomach
18	chr19:18080200-18095200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links