Variant report

Variant	rs1065356
Chromosome Location	chr6:31687008-31687009
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:11)
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	SP1	chr6:31685801-31687042	HCT-116	colon:	n/a	chr6:31686206-31686216 chr6:31686206-31686216 chr6:31686307-31686321
2	POLR2A	chr6:31686918-31687032	MCF-7	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31684754..31687039-chr6:32937262..32940105,2	MCF-7	breast:
2	chr6:31685559..31688052-chr6:31762150..31763709,2	MCF-7	breast:
3	chr6:31635402..31638010-chr6:31685424..31687042,2	MCF-7	breast:
4	chr6:31632296..31634965-chr6:31685541..31687886,2	MCF-7	breast:
5	chr6:31685179..31687517-chr6:31710314..31712214,2	MCF-7	breast:
6	chr6:31686048..31689889-chr6:31795401..31797897,4	MCF-7	breast:
7	chr6:31684407..31687044-chr6:31706148..31707920,2	MCF-7	breast:
8	chr6:31684792..31688095-chr6:31761930..31764765,3	MCF-7	breast:
9	chr6:31685534..31689967-chr6:31702544..31705523,6	MCF-7	breast:
10	chr6:31668227..31672274-chr6:31683898..31689448,8	MCF-7	breast:
11	chr6:31686463..31688392-chr6:31828032..31830692,2	K562	blood:

No data

Variant related genes	Relation type
C6orf25	TF binding region
ENSG00000204435	Chromatin interaction
ENSG00000204410	Chromatin interaction
ENSG00000240053	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000255152	Chromatin interaction
ENSG00000266776	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000213719	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000204386	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204394	Chromatin interaction
ENSG00000204388	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs15574	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs805285	0.87[EUR][1000 genomes]
rs805292	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
12	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
13	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
14	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1065356	C6orf48	cis	multi-tissue	Pritchard
rs1065356	HSPA1B	cis	multi-tissue	Pritchard
rs1065356	AIF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31671800-31695800	Weak transcription	Right Atrium	heart
2	chr6:31679200-31687800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:31679400-31691200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:31682000-31692800	Weak transcription	HSMMtube	muscle
5	chr6:31682000-31693800	Weak transcription	Fetal Kidney	kidney
6	chr6:31682200-31693400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:31682400-31692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:31682400-31693600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:31682400-31693600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:31682400-31696400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:31683000-31693400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:31683200-31693200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:31683200-31693400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:31683200-31696200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:31683400-31692800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:31683600-31689200	Weak transcription	Brain Germinal Matrix	brain
17	chr6:31683600-31689800	Weak transcription	Fetal Stomach	stomach
18	chr6:31683600-31690000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:31683600-31693800	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:31683800-31688800	Weak transcription	Fetal Brain Female	brain
21	chr6:31683800-31691200	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:31684000-31693400	Weak transcription	Fetal Lung	lung
23	chr6:31685000-31687400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:31685200-31687200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr6:31685200-31687200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:31685200-31687200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr6:31685200-31687200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:31685200-31687200	Enhancers	Colonic Mucosa	Colon
29	chr6:31685200-31687200	Enhancers	Fetal Intestine Large	intestine
30	chr6:31685200-31687200	Enhancers	Placenta	Placenta
31	chr6:31685200-31687400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:31685200-31687400	Enhancers	Esophagus	oesophagus
33	chr6:31685200-31688200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr6:31685200-31688800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:31685200-31688800	Enhancers	Stomach Mucosa	stomach
36	chr6:31685200-31688800	Enhancers	HMEC	breast
37	chr6:31685200-31689600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr6:31685400-31687200	Enhancers	Gastric	stomach
39	chr6:31685400-31687400	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr6:31685600-31687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:31685800-31696200	Weak transcription	Brain Anterior Caudate	brain
42	chr6:31686000-31690800	Weak transcription	K562	blood
43	chr6:31686200-31687200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:31686200-31693600	Weak transcription	Aorta	Aorta
45	chr6:31686400-31695600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:31686600-31687200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:31686600-31688600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:31686800-31687200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:31686800-31688600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:31686800-31689000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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