Variant report

Variant	rs3117578
Chromosome Location	chr6:31636031-31636032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31635965-31636562	K562	blood:	n/a	n/a
2	POLR2A	chr6:31635844-31637824	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31632734..31637057-chr6:31703384..31706202,6	MCF-7	breast:
2	chr6:31634033..31636196-chr6:31925448..31927170,2	K562	blood:
3	chr6:31635402..31638010-chr6:31685424..31687042,2	MCF-7	breast:
4	chr6:31511934..31514047-chr6:31634162..31636336,2	MCF-7	breast:
5	chr6:31507927..31511187-chr6:31633283..31638231,4	MCF-7	breast:

No data

Variant related genes	Relation type
GPANK1	TF binding region
LY6G5B	TF binding region
ENSG00000263020	TF binding region
ENSG00000204351	Chromatin interaction
ENSG00000265236	Chromatin interaction
ENSG00000234006	Chromatin interaction
ENSG00000204356	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000204420	Chromatin interaction
ENSG00000213719	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2736177	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2857594	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857600	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2857609	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2857700	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3115668	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3115669	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3130050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130068	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3130071	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130625	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3131377	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9267551	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
12	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
13	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS 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 miRNA target site	326 gene(s)	inside rSNPs	diseases
14	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
15	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3117578	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs3117578	HLA-DQB1	cis	lymphoblastoid	seeQTL
rs3117578	HLA-C	cis	lymphoblastoid	GTEx
rs3117578	HLA-DRB5	cis	lymphoblastoid	GTEx
rs3117578	HLA-DRB5	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31634200-31640000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:31634600-31639800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31634800-31636200	Weak transcription	Aorta	Aorta
4	chr6:31634800-31636200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:31634800-31636400	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:31634800-31636800	Weak transcription	Stomach Mucosa	stomach
7	chr6:31634800-31637000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:31634800-31637000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:31634800-31637400	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr6:31634800-31638800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:31634800-31641400	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr6:31634800-31641400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:31634800-31641400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:31634800-31641400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:31634800-31648200	Weak transcription	Right Atrium	heart
16	chr6:31635000-31636200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:31635000-31636200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:31635000-31636200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr6:31635000-31636200	Genic enhancers	Adipose Nuclei	Adipose
20	chr6:31635000-31636200	Genic enhancers	Duodenum Mucosa	Duodenum
21	chr6:31635000-31636200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
22	chr6:31635000-31636200	Genic enhancers	Fetal Thymus	thymus
23	chr6:31635000-31636200	Genic enhancers	Rectal Mucosa Donor 31	rectum
24	chr6:31635000-31636200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:31635000-31636400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:31635000-31636600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:31635000-31637000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:31635000-31637400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:31635000-31637400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:31635000-31637400	Strong transcription	A549	lung
31	chr6:31635000-31637600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:31635000-31637800	Genic enhancers	HepG2	liver
33	chr6:31635000-31640200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:31635000-31640800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:31635000-31641400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:31635000-31641400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:31635000-31641400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:31635000-31641400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:31635000-31641400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr6:31635000-31641800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr6:31635000-31641800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr6:31635000-31642000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:31635000-31642000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:31635000-31642000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr6:31635000-31642000	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:31635000-31642000	Strong transcription	Spleen	Spleen
47	chr6:31635000-31642200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr6:31635000-31642800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:31635000-31642800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:31635000-31643800	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links