Variant report

Variant	rs3798916
Chromosome Location	chr6:161515383-161515384
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161514750..161517453-chr6:161536334..161537925,2	K562	blood:
2	chr6:161505679..161509602-chr6:161513922..161516452,3	K562	blood:
3	chr6:161514034..161515549-chr6:161518422..161522135,3	K562	blood:
4	chr6:161457964..161460200-chr6:161515366..161517538,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085511	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1001421	1.00[CHB][hapmap]
rs1001422	1.00[CHB][hapmap]
rs1001756	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10080650	1.00[YRI][hapmap]
rs11751634	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs11751688	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11751843	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752188	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs11753446	1.00[AMR][1000 genomes]
rs11755042	1.00[AMR][1000 genomes]
rs11755244	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11757223	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs11757309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs11758794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759000	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759408	1.00[CHB][hapmap];0.87[AMR][1000 genomes]
rs11962121	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs12110827	1.00[CHB][hapmap]
rs12333027	1.00[YRI][hapmap]
rs1404269	1.00[CHB][hapmap]
rs1464781	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534020	1.00[CHB][hapmap]
rs1562025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1807426	1.00[CHB][hapmap]
rs2009830	1.00[CHB][hapmap]
rs2314190	1.00[CHB][hapmap]
rs2314376	1.00[CHB][hapmap]
rs2314377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778225	1.00[CHB][hapmap]
rs3823057	1.00[CHB][hapmap]
rs41268545	0.87[AMR][1000 genomes]
rs55799452	0.87[AMR][1000 genomes]
rs57922639	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58040353	1.00[AMR][1000 genomes]
rs59129068	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59318837	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60649875	0.89[EUR][1000 genomes]
rs6905734	1.00[CHB][hapmap]
rs6907956	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922534	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs719474	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754215	1.00[CHB][hapmap]
rs9365245	1.00[CHB][hapmap]
rs9456621	1.00[YRI][hapmap]
rs9456635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9456636	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9458112	1.00[YRI][hapmap]
rs9458116	0.81[AFR][1000 genomes]
rs9458120	1.00[YRI][hapmap]
rs9458121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9458135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9458141	1.00[CHB][hapmap]

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	nsv1030045	chr6:161359075-161562255	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1023982	chr6:161382188-161549831	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 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	chr6:161486200-161519200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:161491000-161538400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:161491600-161516400	Strong transcription	Placenta	Placenta
4	chr6:161491600-161525400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:161491600-161528800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr6:161491600-161529000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:161491600-161539800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:161493800-161521400	Strong transcription	Fetal Thymus	thymus
9	chr6:161494400-161515400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:161494400-161525600	Strong transcription	Dnd41	blood
11	chr6:161494400-161542400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr6:161495200-161538000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:161495400-161515400	Strong transcription	Fetal Lung	lung
14	chr6:161495400-161516400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:161496000-161539800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:161497800-161539600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:161498000-161541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:161498200-161515400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:161498600-161525600	Strong transcription	Primary T cells from cord blood	blood
20	chr6:161499000-161531800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:161499200-161515400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:161499200-161517000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr6:161499800-161515600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:161499800-161521600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:161500200-161540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:161500400-161515400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:161500400-161517000	Strong transcription	Liver	Liver
28	chr6:161500400-161525600	Strong transcription	Adipose Nuclei	Adipose
29	chr6:161500600-161539800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr6:161500600-161541800	Strong transcription	K562	blood
31	chr6:161500800-161515400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:161500800-161538200	Strong transcription	Primary B cells from cord blood	blood
33	chr6:161501000-161515800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:161501000-161517000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:161501200-161516000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:161502600-161531600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:161503200-161532000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:161503800-161516800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:161504800-161531800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr6:161505000-161524200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:161505000-161524400	Weak transcription	Psoas Muscle	Psoas
42	chr6:161505000-161528200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:161505800-161529800	Weak transcription	Fetal Brain Male	brain
44	chr6:161506600-161515400	Strong transcription	HepG2	liver
45	chr6:161507000-161524000	Weak transcription	A549	lung
46	chr6:161508600-161515400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:161509200-161519000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:161509400-161528000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:161510000-161520800	Weak transcription	Hela-S3	cervix
50	chr6:161510200-161518800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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