Variant report

Variant	rs3798477
Chromosome Location	chr6:36951061-36951062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36930754..36936310-chr6:36950773..36956274,7	MCF-7	breast:
2	chr6:36937337..36939387-chr6:36947202..36951298,3	MCF-7	breast:
3	chr6:36950922..36953739-chr6:37176914..37178749,2	MCF-7	breast:
4	chr6:36949522..36951437-chr6:36961267..36963379,2	K562	blood:
5	chr6:36646638..36649501-chr6:36950264..36953112,2	MCF-7	breast:
6	chr6:36949230..36952224-chr6:37136925..37139369,2	K562	blood:
7	chr6:36853647..36856578-chr6:36948651..36952350,3	K562	blood:

Variant related genes	Relation type
ENSG00000164530	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000137193	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11751297	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11759019	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12191672	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12199301	1.00[JPT][hapmap]
rs16868759	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17624546	1.00[CHB][hapmap]
rs17624895	1.00[CHB][hapmap]
rs2293388	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2293389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3778022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3778024	1.00[JPT][hapmap]
rs3798475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6930271	0.81[CEU][hapmap];0.88[GIH][hapmap]
rs726819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs734905	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs753634	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs753635	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9357232	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9380629	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5263	chr6:36941625-36972109	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
5	esv988069	chr6:36942299-36951067	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv518386	chr6:36942746-37037670	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3798477	PI16	cis	cerebellum	SCAN
rs3798477	CD244	trans	lymphoblastoid	seeQTL
rs3798477	PI16	cis	parietal	SCAN
rs3798477	FILIP1	trans	lymphoblastoid	seeQTL
rs3798477	ZFAND3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36932400-36951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:36934000-36951600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:36939000-36951200	Strong transcription	HSMM	muscle
4	chr6:36945000-36951200	Enhancers	Fetal Heart	heart
5	chr6:36945400-36951400	Weak transcription	Fetal Kidney	kidney
6	chr6:36946200-36952000	Weak transcription	A549	lung
7	chr6:36946400-36951200	Weak transcription	Hela-S3	cervix
8	chr6:36946400-36951600	Weak transcription	HSMMtube	muscle
9	chr6:36946400-36951800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:36946600-36951200	Weak transcription	HMEC	breast
11	chr6:36946800-36951800	Enhancers	Brain Angular Gyrus	brain
12	chr6:36946800-36951800	Genic enhancers	Brain Anterior Caudate	brain
13	chr6:36947000-36951400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
14	chr6:36947200-36952000	Enhancers	Colon Smooth Muscle	Colon
15	chr6:36947400-36951200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:36947600-36951200	Weak transcription	NH-A	brain
17	chr6:36947600-36951600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:36947600-36951800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:36947800-36951200	Genic enhancers	Dnd41	blood
20	chr6:36948800-36951400	Weak transcription	NHEK	skin
21	chr6:36949200-36951800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr6:36949200-36951800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:36949200-36952400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:36949400-36951200	Enhancers	Right Ventricle	heart
25	chr6:36949400-36951200	Strong transcription	Thymus	Thymus
26	chr6:36949400-36951400	Weak transcription	Fetal Brain Male	brain
27	chr6:36949400-36951600	Weak transcription	Psoas Muscle	Psoas
28	chr6:36949400-36951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:36949400-36951800	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:36949400-36951800	Weak transcription	Placenta	Placenta
31	chr6:36949400-36952400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:36949600-36951200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:36949600-36951200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:36949600-36951200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:36949600-36951400	Weak transcription	Gastric	stomach
36	chr6:36949600-36951600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:36949600-36952200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr6:36949800-36951400	Weak transcription	Left Ventricle	heart
39	chr6:36949800-36951600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:36949800-36951600	Weak transcription	Brain Germinal Matrix	brain
41	chr6:36949800-36951600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:36949800-36951800	Enhancers	Primary T cells from cord blood	blood
43	chr6:36949800-36952400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr6:36950000-36951200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:36950000-36951600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:36950000-36951600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr6:36950000-36951800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:36950000-36951800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:36950200-36952200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:36950200-36952200	Enhancers	Right Atrium	heart

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