Variant report

Variant	rs35404791
Chromosome Location	chr16:71945847-71945848
allele	C/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	POLR2A	chr16:71945724-71946088	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:71945768-71946009	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:71945546-71945989	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:71945530-71945932	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:71945749-71946030	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:71945808-71946054	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:71928128..71930388-chr16:71945067..71946732,2	MCF-7	breast:
2	chr16:71945578..71947499-chr16:71964859..71966489,2	MCF-7	breast:
3	chr16:71945008..71946911-chr16:71957632..71959636,2	MCF-7	breast:

Variant related genes	Relation type
IST1	TF binding region
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10500567	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852507	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075906	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11639843	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640135	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11644740	0.85[ASN][1000 genomes]
rs11865456	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149307	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149325	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149917	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12445564	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445641	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448086	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12921279	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12921459	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12927691	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934512	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330178	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17357420	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17358402	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878494	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3088285	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34029919	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101687	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664834	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35028754	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35069141	0.81[ASN][1000 genomes]
rs35209006	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35377660	0.84[EUR][1000 genomes]
rs35535529	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35595148	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36182990	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751820	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528577	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71384781	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71384782	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71386939	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71386940	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71386942	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7185027	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7188591	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7191848	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195988	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197486	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7198834	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73586164	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8046044	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs8049508	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050058	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052358	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8053906	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs8063657	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9940234	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking 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	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71930800-71950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:71930800-71951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:71931000-71949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr16:71931000-71949600	Weak transcription	NHEK	skin
5	chr16:71931200-71946600	Weak transcription	A549	lung
6	chr16:71931200-71949800	Weak transcription	Esophagus	oesophagus
7	chr16:71931200-71950000	Weak transcription	HMEC	breast
8	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr16:71931400-71949400	Weak transcription	Fetal Kidney	kidney
10	chr16:71932600-71951800	Weak transcription	Colonic Mucosa	Colon
11	chr16:71933400-71948400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr16:71933400-71949000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr16:71933400-71950200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr16:71934200-71949600	Weak transcription	Placenta	Placenta
15	chr16:71934400-71951000	Weak transcription	Fetal Brain Male	brain
16	chr16:71934600-71946600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr16:71934600-71948400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr16:71934600-71948800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr16:71934600-71949000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr16:71934600-71949600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr16:71934800-71946600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr16:71934800-71948200	Weak transcription	HUVEC	blood vessel
23	chr16:71935000-71946600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr16:71935200-71950200	Weak transcription	NHLF	lung
25	chr16:71936000-71948200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr16:71936000-71948600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr16:71936200-71946600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr16:71937200-71952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr16:71937600-71947400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr16:71938000-71949800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr16:71938600-71948200	Weak transcription	Brain Substantia Nigra	brain
32	chr16:71939200-71949800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr16:71940000-71946600	Weak transcription	Primary B cells from cord blood	blood
34	chr16:71940600-71950000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr16:71941000-71950000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr16:71941400-71950000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr16:71941800-71948400	Strong transcription	Fetal Stomach	stomach
38	chr16:71942200-71951400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr16:71942200-71951600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr16:71942600-71946000	Genic enhancers	HepG2	liver
41	chr16:71942800-71946600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr16:71943400-71946200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr16:71943400-71946800	Weak transcription	Brain Hippocampus Middle	brain
44	chr16:71943400-71947000	Weak transcription	Psoas Muscle	Psoas
45	chr16:71943400-71948400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:71943400-71949200	Weak transcription	Thymus	Thymus
47	chr16:71943400-71949800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr16:71943400-71949800	Weak transcription	Lung	lung
49	chr16:71943400-71949800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr16:71943400-71950000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links