Variant report

Variant	rs7190997
Chromosome Location	chr16:31368178-31368179
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	JUND	chr16:31368017-31368372	H1-hESC	embryonic stem cell:	n/a	chr16:31368050-31368059 chr16:31368048-31368059
2	FOSL2	chr16:31367888-31368230	HepG2	liver:	n/a	chr16:31368050-31368059
3	RAD21	chr16:31368170-31368504	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr16:31368067-31368562	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr16:31368160-31368310	GM12866	blood:	n/a	n/a
6	CTCF	chr16:31368177-31368524	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr16:31368149-31368529	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31190496..31192214-chr16:31368075..31369676,2	MCF-7	breast:
2	chr16:31366361..31368060-chr16:31368172..31370932,2	MCF-7	breast:

Variant related genes	Relation type
ITGAX	TF binding region
ENSG00000140678	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10747210	0.81[ASN][1000 genomes]
rs10782004	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1106398	0.96[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11150611	0.84[ASN][1000 genomes]
rs11150612	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11150613	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11150614	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs11150616	0.92[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11150617	0.94[ASN][1000 genomes]
rs11150619	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11574630	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11574631	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11574639	0.94[ASN][1000 genomes]
rs11645917	0.83[ASN][1000 genomes]
rs11859274	0.83[ASN][1000 genomes]
rs12923297	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12935192	0.83[ASN][1000 genomes]
rs13332545	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2230429	0.84[ASN][1000 genomes]
rs3087796	0.83[CHB][hapmap]
rs4077810	0.86[CHB][hapmap]
rs4459557	0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4493054	0.83[ASN][1000 genomes]
rs4506917	0.90[JPT][hapmap]
rs4597342	0.86[CHB][hapmap]
rs4889649	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs56392848	0.84[ASN][1000 genomes]
rs7206295	0.86[CHB][hapmap]
rs8060268	0.86[CHB][hapmap]
rs9673519	0.89[CHB][hapmap];0.93[JPT][hapmap]

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	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7190997	YPEL3	cis	cerebellum	SCAN
rs7190997	MYST1	cis	cerebellum	SCAN
rs7190997	TBX6	cis	parietal	SCAN
rs7190997	PRSS53	cis	Esophagus Muscularis	GTEx
rs7190997	ITGAX	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31343000-31400800	Weak transcription	Right Atrium	heart
2	chr16:31363800-31368200	Weak transcription	Fetal Muscle Leg	muscle
3	chr16:31364400-31370200	Enhancers	Primary T cells fromperipheralblood	blood
4	chr16:31365600-31368600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr16:31365600-31369200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:31365600-31369800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr16:31366000-31368800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr16:31366400-31368200	Active TSS	Adipose Nuclei	Adipose
9	chr16:31366400-31369200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr16:31366600-31368200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr16:31366600-31369800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr16:31366600-31369800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr16:31366800-31368200	Weak transcription	Colonic Mucosa	Colon
14	chr16:31366800-31368400	Weak transcription	Fetal Thymus	thymus
15	chr16:31366800-31368800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr16:31366800-31368800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr16:31366800-31369000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr16:31366800-31369200	Weak transcription	Lung	lung
19	chr16:31367000-31368200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr16:31367000-31368800	Enhancers	Primary hematopoietic stem cells	blood
21	chr16:31367000-31370000	Enhancers	Primary B cells from peripheral blood	blood
22	chr16:31367400-31368600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr16:31367400-31368600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr16:31367400-31368600	Weak transcription	GM12878-XiMat	blood
25	chr16:31367800-31368800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr16:31367800-31369600	Genic enhancers	Spleen	Spleen
27	chr16:31368000-31368200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr16:31368000-31368200	Enhancers	A549	lung
29	chr16:31368000-31368400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr16:31368000-31368400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr16:31368000-31368600	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr16:31368000-31368800	Active TSS	Primary B cells from cord blood	blood
33	chr16:31368000-31369000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr16:31368000-31369600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood

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