Variant report

Variant	rs28436203
Chromosome Location	chr16:71796404-71796405
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	GATA2	chr16:71796074-71796598	HUVEC	blood vessel:	n/a	n/a
2	STAT3	chr16:71796043-71796421	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr16:71796082-71796432	IMR90	lung:	n/a	n/a
4	POLR2A	chr16:71795850-71796443	K562	blood:	n/a	n/a
5	STAT3	chr16:71796087-71796407	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr16:71795836-71796779	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:71795022..71797414-chr16:71798658..71803314,4	MCF-7	breast:
2	chr16:71796071..71798495-chr16:71805042..71807418,2	MCF-7	breast:

Variant related genes	Relation type
SNORD71	TF binding region
ENSG00000166747	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11075896	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11075897	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13331951	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333988	1.00[AMR][1000 genomes]
rs13334187	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334255	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334566	0.88[AFR][1000 genomes]
rs13337119	0.86[AFR][1000 genomes]
rs13337224	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338265	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338868	0.88[LWK][hapmap]
rs28487278	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556848	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28649987	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28711364	0.83[AFR][1000 genomes]
rs28712876	1.00[AMR][1000 genomes]
rs28757746	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34113755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55829421	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55930830	1.00[AMR][1000 genomes]
rs57187537	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58324033	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60173154	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6499544	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs7186536	0.93[AFR][1000 genomes]
rs7191105	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs7196013	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7198645	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7202000	0.83[AFR][1000 genomes]
rs73578257	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73580232	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582208	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582231	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582271	0.95[AFR][1000 genomes]
rs73582274	0.95[AFR][1000 genomes]
rs73582278	0.95[AFR][1000 genomes]
rs73582282	0.95[AFR][1000 genomes]
rs73584107	0.86[AFR][1000 genomes]
rs8045394	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs8048170	1.00[AMR][1000 genomes]
rs8051461	0.84[YRI][hapmap]
rs8059131	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062948	1.00[AMR][1000 genomes]
rs8063658	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9302626	0.89[YRI][hapmap]
rs9302628	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921383	1.00[ASW][hapmap];0.94[MKK][hapmap]
rs9923154	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9924829	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9925712	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9927004	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928298	1.00[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928788	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930271	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930573	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930588	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933587	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933862	0.93[AFR][1000 genomes]
rs9934778	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935867	0.86[AFR][1000 genomes];1.00[AMR][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	esv1817133	chr16:71705908-71837477	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	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
4	esv1819402	chr16:71755852-71816899	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	n/a
5	esv1815957	chr16:71790812-71816899	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28436203	MARVELD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71761000-71805600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:71762200-71811400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:71763200-71799800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:71763200-71812600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr16:71763400-71802200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr16:71763600-71800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr16:71763600-71801400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr16:71763600-71812400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr16:71763800-71799600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr16:71763800-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr16:71764000-71804800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr16:71764000-71813000	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr16:71764800-71802600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr16:71770600-71798600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr16:71770600-71799600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr16:71770800-71799600	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr16:71770800-71810600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr16:71770800-71813800	Strong transcription	Liver	Liver
19	chr16:71771000-71812200	Strong transcription	Placenta	Placenta
20	chr16:71777200-71799800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr16:71779600-71841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:71780000-71821400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:71783800-71820600	Weak transcription	Psoas Muscle	Psoas
24	chr16:71784000-71811200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:71785400-71799800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr16:71785400-71808800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr16:71786400-71799800	Strong transcription	Adipose Nuclei	Adipose
28	chr16:71786400-71802200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr16:71786400-71805200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr16:71786600-71809800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr16:71786800-71797200	Strong transcription	Primary T cells from cord blood	blood
32	chr16:71786800-71797600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:71787000-71797400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr16:71787000-71799800	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr16:71787000-71802200	Strong transcription	Fetal Thymus	thymus
36	chr16:71787200-71797200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr16:71787200-71797200	Strong transcription	Fetal Muscle Leg	muscle
38	chr16:71787200-71797200	Strong transcription	Fetal Stomach	stomach
39	chr16:71787200-71797200	Strong transcription	Thymus	Thymus
40	chr16:71787200-71798600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr16:71787200-71799600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr16:71787200-71799800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr16:71787200-71800000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr16:71788000-71806600	Weak transcription	Stomach Mucosa	stomach
45	chr16:71789800-71802200	Strong transcription	GM12878-XiMat	blood
46	chr16:71792600-71797000	Weak transcription	K562	blood
47	chr16:71792600-71801000	Weak transcription	Fetal Brain Female	brain
48	chr16:71792600-71806600	Weak transcription	Fetal Brain Male	brain
49	chr16:71792800-71796600	Weak transcription	Brain Angular Gyrus	brain
50	chr16:71792800-71797200	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links