Variant report

Variant	rs4788578
Chromosome Location	chr16:71938372-71938373
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71931560..71934913-chr16:71937416..71939939,3	K562	blood:
2	chr16:71936147..71938955-chr16:71940995..71943560,3	K562	blood:
3	chr16:71926844..71931687-chr16:71933054..71938868,11	MCF-7	breast:
4	chr16:71935084..71939148-chr16:71940742..71943811,5	MCF-7	breast:
5	chr16:71933462..71935893-chr16:71936421..71939134,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1035543	0.89[EUR][1000 genomes]
rs12597418	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12600153	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12600163	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13332113	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13332180	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13337118	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1834033	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291947	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34111614	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4538017	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4788448	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788567	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4788572	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788574	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55702379	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56309616	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60075093	0.92[EUR][1000 genomes]
rs60740701	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7350856	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8058762	0.82[ASN][1000 genomes]
rs952159	0.94[EUR][1000 genomes]
rs952160	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9889100	0.87[EUR][1000 genomes]
rs9925441	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9925684	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9936965	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9937626	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71930800-71943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr16:71930800-71944200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr16:71930800-71950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:71930800-71951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr16:71931000-71942800	Weak transcription	Fetal Heart	heart
6	chr16:71931000-71949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:71931000-71949600	Weak transcription	NHEK	skin
8	chr16:71931200-71940600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr16:71931200-71942800	Weak transcription	HSMM	muscle
10	chr16:71931200-71943000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr16:71931200-71943000	Weak transcription	Fetal Lung	lung
12	chr16:71931200-71943000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr16:71931200-71943200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr16:71931200-71944800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr16:71931200-71946600	Weak transcription	A549	lung
16	chr16:71931200-71949800	Weak transcription	Esophagus	oesophagus
17	chr16:71931200-71950000	Weak transcription	HMEC	breast
18	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr16:71931400-71942600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr16:71931400-71949400	Weak transcription	Fetal Kidney	kidney
21	chr16:71931600-71942400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr16:71931600-71944400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr16:71932000-71942600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr16:71932000-71942600	Weak transcription	Thymus	Thymus
25	chr16:71932000-71942800	Weak transcription	Hela-S3	cervix
26	chr16:71932000-71943200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr16:71932400-71943000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:71932600-71942600	Weak transcription	Gastric	stomach
29	chr16:71932600-71951800	Weak transcription	Colonic Mucosa	Colon
30	chr16:71932800-71942600	Weak transcription	Fetal Thymus	thymus
31	chr16:71933200-71942600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr16:71933400-71940400	Weak transcription	Fetal Muscle Leg	muscle
33	chr16:71933400-71942600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr16:71933400-71948400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr16:71933400-71949000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr16:71933400-71950200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:71934000-71943000	Weak transcription	Lung	lung
38	chr16:71934200-71949600	Weak transcription	Placenta	Placenta
39	chr16:71934400-71938400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr16:71934400-71939000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr16:71934400-71943000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr16:71934400-71945600	Weak transcription	Aorta	Aorta
43	chr16:71934400-71951000	Weak transcription	Fetal Brain Male	brain
44	chr16:71934600-71942000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:71934600-71942400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr16:71934600-71943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr16:71934600-71943200	Weak transcription	NHDF-Ad	bronchial
48	chr16:71934600-71943400	Weak transcription	Colon Smooth Muscle	Colon
49	chr16:71934600-71946600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr16:71934600-71948400	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links