Variant report

Variant	rs11871642
Chromosome Location	chr17:19549123-19549124
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	RAD21	chr17:19548982-19549498	Hela-S3	cervix:	n/a	n/a
2	RAD21	chr17:19549107-19549540	MCF-7	breast:	n/a	n/a
3	CTCF	chr17:19549114-19549616	HCT-116	colon:	n/a	n/a
4	RAD21	chr17:19549063-19549586	HCT-116	colon:	n/a	n/a
5	JUND	chr17:19549054-19549449	K562	blood:	n/a	chr17:19549124-19549133
6	CTCF	chr17:19549115-19549642	A549	lung:	n/a	n/a
7	CTCF	chr17:19547863-19549782	A549	lung:	n/a	n/a
8	CTCF	chr17:19548949-19549636	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr17:19549015-19549176	SH-SY5Y	brain:	n/a	n/a
10	RAD21	chr17:19549122-19549617	H1-hESC	embryonic stem cell:	n/a	n/a
11	RAD21	chr17:19549066-19549666	A549	lung:	n/a	n/a
12	RAD21	chr17:19549078-19549679	ECC-1	luminal epithelium:	n/a	n/a
13	PRDM1	chr17:19548970-19549400	Hela-S3	cervix:	n/a	chr17:19549206-19549220 chr17:19549291-19549305 chr17:19549205-19549220 chr17:19549292-19549301
14	CTCF	chr17:19549000-19549150	GM12878	blood:	n/a	n/a
15	YY1	chr17:19549118-19549582	H1-hESC	embryonic stem cell:	n/a	n/a
16	JUN	chr17:19549004-19549254	HepG2	liver:	n/a	chr17:19549124-19549133 chr17:19549123-19549136
17	RAD21	chr17:19548520-19549773	SK-N-SH	brain:	n/a	n/a
18	JUND	chr17:19548949-19549320	HepG2	liver:	n/a	chr17:19549124-19549133

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19549032..19550747-chr17:19657076..19658934,2	MCF-7	breast:

Variant related genes	Relation type
ALDH3A2	TF binding region
ENSG00000230607	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3744692	1.00[JPT][hapmap]
rs3744694	1.00[JPT][hapmap]
rs4646783	1.00[JPT][hapmap]
rs57138841	0.90[ASN][1000 genomes]
rs8068565	1.00[TSI][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	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv2757654	chr17:19485735-19563766	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	esv2758679	chr17:19485735-19563766	Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1055361	chr17:19515267-19582503	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19538000-19549400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:19545400-19549600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:19545600-19550400	Enhancers	HepG2	liver
4	chr17:19545800-19550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:19546000-19549800	Weak transcription	HMEC	breast
6	chr17:19546200-19550400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:19546400-19549400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:19547000-19550200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:19547200-19549400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:19547400-19551800	Flanking Active TSS	Liver	Liver
11	chr17:19547600-19550200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:19548000-19551000	Enhancers	Stomach Mucosa	stomach
13	chr17:19548200-19549200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:19548200-19549600	Enhancers	Small Intestine	intestine
15	chr17:19548200-19549800	Weak transcription	Fetal Intestine Large	intestine
16	chr17:19548200-19550400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr17:19548200-19550800	Enhancers	Adipose Nuclei	Adipose
18	chr17:19548200-19550800	Enhancers	Osteobl	bone
19	chr17:19548200-19551000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr17:19548400-19550000	Weak transcription	Fetal Intestine Small	intestine
21	chr17:19548400-19550400	Weak transcription	Placenta	Placenta
22	chr17:19548400-19550800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr17:19548400-19550800	Enhancers	Stomach Smooth Muscle	stomach
24	chr17:19548600-19549200	Enhancers	Colon Smooth Muscle	Colon
25	chr17:19548600-19550000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr17:19548600-19550000	Weak transcription	NHEK	skin
27	chr17:19548600-19550400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr17:19548800-19549400	Enhancers	Psoas Muscle	Psoas
29	chr17:19548800-19549600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
30	chr17:19548800-19549600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr17:19548800-19550000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr17:19548800-19550200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:19548800-19551000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr17:19548800-19551200	Enhancers	Fetal Heart	heart
35	chr17:19548800-19551600	Flanking Active TSS	Hela-S3	cervix
36	chr17:19549000-19549200	Enhancers	Brain Cingulate Gyrus	brain
37	chr17:19549000-19549200	Enhancers	Brain Substantia Nigra	brain
38	chr17:19549000-19549400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr17:19549000-19549400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
40	chr17:19549000-19549400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr17:19549000-19549400	Flanking Active TSS	A549	lung
42	chr17:19549000-19549600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr17:19549000-19549600	Enhancers	Brain Anterior Caudate	brain
44	chr17:19549000-19549800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr17:19549000-19549800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
46	chr17:19549000-19550000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr17:19549000-19550800	Enhancers	Duodenum Mucosa	Duodenum

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