Variant report

Variant	rs55769835
Chromosome Location	chr16:70475531-70475532
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	ATF1	chr16:70475520-70475796	K562	blood:	n/a	n/a
2	JUND	chr16:70475488-70475814	K562	blood:	n/a	n/a
3	JUND	chr16:70475512-70475810	HepG2	liver:	n/a	n/a
4	MBD4	chr16:70475323-70475871	HepG2	liver:	n/a	n/a
5	RCOR1	chr16:70475511-70475832	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:70473375..70475549-chr16:70479370..70482339,3	MCF-7	breast:
2	chr16:70470745..70475630-chr16:70476191..70481668,5	MCF-7	breast:

Variant related genes	Relation type
ST3GAL2	TF binding region
ENSG00000240043	Chromatin interaction
ENSG00000200153	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs11859191	1.00[EUR][1000 genomes]
rs11859870	0.92[AMR][1000 genomes]
rs11861486	0.92[AMR][1000 genomes]
rs11862150	1.00[EUR][1000 genomes]
rs11862188	1.00[EUR][1000 genomes]
rs11863943	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11864179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11864326	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11865484	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11865564	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970121	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16970133	0.92[AMR][1000 genomes]
rs16970141	0.83[AMR][1000 genomes]
rs16970147	1.00[EUR][1000 genomes]
rs16970149	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970151	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970152	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970153	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970159	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs16970165	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16970169	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs16970302	1.00[EUR][1000 genomes]
rs17878609	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17878832	1.00[EUR][1000 genomes]
rs17879665	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17880242	1.00[EUR][1000 genomes]
rs17880268	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17881069	1.00[EUR][1000 genomes]
rs17881219	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17883309	1.00[EUR][1000 genomes]
rs17886064	1.00[EUR][1000 genomes]
rs3096368	1.00[EUR][1000 genomes]
rs35904382	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4999488	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs55657328	1.00[EUR][1000 genomes]
rs55775924	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55805938	1.00[EUR][1000 genomes]
rs55819743	1.00[EUR][1000 genomes]
rs55916527	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55936739	1.00[EUR][1000 genomes]
rs56050266	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56082018	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56348821	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56836664	0.92[AMR][1000 genomes]
rs56980444	1.00[EUR][1000 genomes]
rs57422630	1.00[EUR][1000 genomes]
rs58047061	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58131227	1.00[EUR][1000 genomes]
rs58328210	1.00[EUR][1000 genomes]
rs58467558	1.00[EUR][1000 genomes]
rs59384897	1.00[EUR][1000 genomes]
rs59552467	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59612351	1.00[EUR][1000 genomes]
rs59928915	0.83[AMR][1000 genomes]
rs60011151	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60045805	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs60387488	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60426209	1.00[EUR][1000 genomes]
rs60646112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61266247	0.83[AMR][1000 genomes]
rs61284127	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61319691	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61369696	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6499312	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6499313	1.00[EUR][1000 genomes]
rs6499314	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6499315	1.00[EUR][1000 genomes]
rs7188864	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7190536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7190921	1.00[EUR][1000 genomes]
rs7192000	1.00[EUR][1000 genomes]
rs7195086	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7195104	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198871	1.00[EUR][1000 genomes]
rs7199346	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7199655	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7203548	0.92[AMR][1000 genomes]
rs7203761	0.92[AMR][1000 genomes]
rs7205918	1.00[EUR][1000 genomes]
rs7206347	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74024182	1.00[EUR][1000 genomes]
rs74024183	1.00[EUR][1000 genomes]
rs74024184	1.00[EUR][1000 genomes]
rs74024185	1.00[EUR][1000 genomes]
rs74024186	1.00[EUR][1000 genomes]
rs74024188	1.00[EUR][1000 genomes]
rs74026022	1.00[EUR][1000 genomes]
rs74026026	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74026033	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74026049	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8045571	1.00[EUR][1000 genomes]
rs8046253	1.00[EUR][1000 genomes]
rs8046662	1.00[EUR][1000 genomes]
rs8046786	1.00[EUR][1000 genomes]
rs8049046	1.00[EUR][1000 genomes]
rs8053657	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8053883	0.92[AMR][1000 genomes]
rs8054203	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8056811	1.00[EUR][1000 genomes]
rs8058735	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062602	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8064090	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482577	chr16:70329048-70516069	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	esv1815154	chr16:70467819-70515355	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2830027	chr16:70473934-70558039	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70473800-70478200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr16:70473800-70478200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr16:70473800-70480600	Weak transcription	Colonic Mucosa	Colon
4	chr16:70473800-70484800	Weak transcription	Right Atrium	heart
5	chr16:70474000-70477200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr16:70474000-70477800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr16:70474000-70478200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr16:70474000-70478400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr16:70474000-70478400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr16:70474000-70478600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr16:70474000-70480800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr16:70474200-70476000	Enhancers	K562	blood
13	chr16:70474200-70477400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr16:70474200-70478200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr16:70474200-70478400	Weak transcription	Stomach Mucosa	stomach
16	chr16:70474200-70478400	Weak transcription	GM12878-XiMat	blood
17	chr16:70474200-70479000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr16:70474200-70479000	Weak transcription	Small Intestine	intestine
19	chr16:70474400-70478200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr16:70474400-70484600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:70474800-70475800	Enhancers	Fetal Intestine Large	intestine
22	chr16:70475000-70475800	Flanking Active TSS	HepG2	liver
23	chr16:70475200-70476400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr16:70475400-70475800	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links