Variant report

Variant	rs7198645
Chromosome Location	chr16:71744839-71744840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71741661..71743207-chr16:71744792..71746297,2	MCF-7	breast:
2	chr16:71744123..71745752-chr16:71748434..71750237,2	K562	blood:
3	chr16:71722834..71724416-chr16:71742268..71745053,2	MCF-7	breast:
4	chr16:71741780..71745597-chr16:71754510..71759356,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000040199	Chromatin interaction
ENSG00000261513	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11075896	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11075897	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13331951	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13333988	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334187	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334255	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13334566	1.00[AFR][1000 genomes]
rs13337162	0.88[AFR][1000 genomes]
rs13337224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338265	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13338868	0.88[LWK][hapmap]
rs13339574	0.83[AFR][1000 genomes]
rs28436203	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]
rs28487278	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556848	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28649987	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28681277	0.85[AFR][1000 genomes]
rs28712876	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28757746	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34113755	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55829421	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55930830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57187537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57827931	0.83[AFR][1000 genomes]
rs58324033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60173154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6499544	1.00[ASW][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs7186536	0.81[AFR][1000 genomes]
rs7191105	0.82[YRI][hapmap]
rs7196013	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73578257	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73580232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582231	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73582271	0.83[AFR][1000 genomes]
rs73582274	0.83[AFR][1000 genomes]
rs73582278	0.83[AFR][1000 genomes]
rs73582282	0.83[AFR][1000 genomes]
rs8045394	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs8048170	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8051461	0.84[YRI][hapmap]
rs8052358	1.00[CHB][hapmap]
rs8059131	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8062948	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8063658	0.90[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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921383	1.00[ASW][hapmap];0.94[MKK][hapmap]
rs9921552	0.88[AFR][1000 genomes]
rs9923154	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9924829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9924862	0.88[AFR][1000 genomes]
rs9925371	0.85[AFR][1000 genomes]
rs9925712	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926077	0.85[AFR][1000 genomes]
rs9927004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928298	1.00[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9928788	0.91[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];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930573	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9930588	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933587	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9933862	0.81[AFR][1000 genomes]
rs9934778	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9935867	0.95[AFR][1000 genomes];1.00[AMR][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	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	nsv1063338	chr16:71612346-71752968	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7198645	MARVELD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71683800-71756600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:71693000-71756400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr16:71702000-71756200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr16:71705000-71756200	Weak transcription	Colon Smooth Muscle	Colon
5	chr16:71705000-71756800	Weak transcription	Gastric	stomach
6	chr16:71707400-71750200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:71710600-71756200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:71710600-71756400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:71710600-71756800	Weak transcription	Lung	lung
10	chr16:71711200-71756400	Weak transcription	K562	blood
11	chr16:71715800-71756000	Weak transcription	Brain Hippocampus Middle	brain
12	chr16:71716800-71756600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr16:71721600-71748400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr16:71724400-71748800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr16:71724400-71756000	Weak transcription	Dnd41	blood
16	chr16:71724400-71756200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr16:71724600-71756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr16:71724800-71756000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:71725000-71756000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr16:71725000-71756600	Weak transcription	Left Ventricle	heart
21	chr16:71727600-71745600	Weak transcription	GM12878-XiMat	blood
22	chr16:71733400-71756600	Weak transcription	Aorta	Aorta
23	chr16:71733800-71745800	Weak transcription	Brain Angular Gyrus	brain
24	chr16:71733800-71745800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr16:71733800-71756000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr16:71734000-71745800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr16:71734000-71756400	Weak transcription	Liver	Liver
28	chr16:71734000-71756600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr16:71734000-71756600	Weak transcription	Thymus	Thymus
30	chr16:71734000-71756800	Weak transcription	Pancreas	Pancrea
31	chr16:71734200-71748200	Weak transcription	Primary T cells from cord blood	blood
32	chr16:71734200-71748400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr16:71734200-71756200	Weak transcription	Fetal Lung	lung
34	chr16:71734400-71747600	Weak transcription	Brain Germinal Matrix	brain
35	chr16:71735000-71755800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr16:71735600-71748000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr16:71736000-71756400	Weak transcription	Brain Substantia Nigra	brain
38	chr16:71736400-71745800	Weak transcription	Brain Anterior Caudate	brain
39	chr16:71736400-71753200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:71736600-71748000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr16:71736600-71756000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr16:71737000-71746800	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr16:71740200-71747400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr16:71741600-71756800	Weak transcription	Small Intestine	intestine
45	chr16:71741800-71745600	Weak transcription	HepG2	liver
46	chr16:71741800-71745800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr16:71741800-71747800	Weak transcription	Fetal Muscle Leg	muscle
48	chr16:71741800-71756600	Weak transcription	Psoas Muscle	Psoas
49	chr16:71742000-71745800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr16:71742000-71746600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links