Variant report

Variant	rs350112
Chromosome Location	chr5:68418577-68418578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68407951..68409881-chr5:68417199..68419048,3	K562	blood:
2	chr5:68407951..68409711-chr5:68417199..68419048,2	K562	blood:
3	chr5:68337237..68339052-chr5:68416019..68418711,2	K562	blood:
4	chr5:68410842..68413494-chr5:68417164..68418893,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145740	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10056618	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs163191	0.91[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs163192	0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs163193	0.94[ASN][1000 genomes]
rs163194	0.92[ASN][1000 genomes]
rs164391	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs164394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164396	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164572	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164577	0.96[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164578	0.92[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164579	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164580	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164581	0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs164710	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164712	0.96[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186790	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187043	0.92[ASN][1000 genomes]
rs234262	0.83[AMR][1000 genomes]
rs240809	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447794	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337253	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337256	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs337259	0.94[ASN][1000 genomes]
rs337262	0.94[ASN][1000 genomes]
rs338668	0.88[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs338678	0.94[ASN][1000 genomes]
rs350110	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs350111	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351444	0.81[CHD][hapmap]
rs420228	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454828	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs570884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688674	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9291940	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv881765	chr5:68379836-68448694	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv881766	chr5:68401941-68448694	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68391400-68428800	Weak transcription	Stomach Mucosa	stomach
2	chr5:68391400-68431200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:68392200-68427000	Weak transcription	Fetal Heart	heart
4	chr5:68395000-68419400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:68395000-68428400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:68397400-68425000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:68397400-68426400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:68397600-68425000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:68398600-68427400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:68398800-68426000	Strong transcription	Adipose Nuclei	Adipose
11	chr5:68399000-68421400	Strong transcription	Osteobl	bone
12	chr5:68399000-68422600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:68399000-68424600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:68399000-68425600	Strong transcription	Fetal Thymus	thymus
15	chr5:68399000-68428200	Strong transcription	Placenta	Placenta
16	chr5:68400200-68431200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:68402600-68429600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:68402800-68427400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:68403000-68425600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:68403600-68426400	Weak transcription	Small Intestine	intestine
21	chr5:68405800-68421800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:68406000-68418800	Weak transcription	Fetal Brain Male	brain
23	chr5:68406000-68419200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:68406000-68427400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:68406000-68430000	Strong transcription	Liver	Liver
26	chr5:68406200-68419000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:68406200-68422200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:68406200-68425400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr5:68406200-68438400	Weak transcription	Aorta	Aorta
30	chr5:68406400-68431600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:68407400-68425600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:68407600-68423800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:68407800-68425800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:68408200-68426400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:68408200-68426600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr5:68408400-68425800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:68408600-68419600	Strong transcription	NHDF-Ad	bronchial
38	chr5:68408800-68419200	Strong transcription	Fetal Muscle Leg	muscle
39	chr5:68409600-68427600	Strong transcription	Fetal Intestine Large	intestine
40	chr5:68410400-68431800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:68411600-68418800	Weak transcription	Fetal Brain Female	brain
42	chr5:68412400-68424800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:68412400-68434600	Weak transcription	Psoas Muscle	Psoas
44	chr5:68412800-68428800	Weak transcription	Colonic Mucosa	Colon
45	chr5:68413200-68418600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:68413200-68419400	Weak transcription	HMEC	breast
47	chr5:68413200-68423000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr5:68413200-68424600	Weak transcription	NHLF	lung
49	chr5:68414200-68419600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:68414200-68419600	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links