Variant report

Variant	rs7560571
Chromosome Location	chr2:95692774-95692775
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:95692691-95693063	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:95692694-95692848	GM12878	blood:	n/a	n/a
3	CTCF	chr2:95692760-95692910	HEK293	kidney:	n/a	chr2:95692896-95692909
4	STAT3	chr2:95692735-95692864	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:95692727-95692777	U87	brain:	n/a
2	chr2:95692727-95692777	HCF	heart:	n/a
3	chr2:95692727-95692777	SK-N-MC	brain:	n/a
4	chr2:95692727-95692777	HRCEpiC	kidney:	n/a
5	chr2:95692727-95692777	LNCaP	prostate:	n/a
6	chr2:95692727-95692777	MCF10A-Er-Src	breast:	n/a
7	chr2:95692727-95692777	NHDF-neo	bronchial:	n/a
8	chr2:95692727-95692777	ECC-1	luminal epithelium:	n/a
9	chr2:95692727-95692777	HEEpiC	esophagus:	n/a
10	chr2:95692727-95692777	GM12891	blood:	n/a
11	chr2:95692727-95692777	MCF-7	breast:	n/a
12	chr2:95692727-95692777	IMR90	lung:	fetal
13	chr2:95692727-95692777	HCT-116	colon:	n/a
14	chr2:95692727-95692777	BJ	skin:	n/a
15	chr2:95692727-95692777	HCM	heart:	n/a
16	chr2:95692727-95692777	ovcar-3	ovarian:	n/a
17	chr2:95692727-95692777	SAEC	small airway:	n/a
18	chr2:95692727-95692777	AG10803	skin:	n/a
19	chr2:95692727-95692777	AG09309	skin:	n/a
20	chr2:95692727-95692777	SKMC	muscle:	n/a
21	chr2:95692727-95692777	PFSK-1	brain:	n/a
22	chr2:95692727-95692777	HCPEpiC	choroid plexus:	n/a
23	chr2:95692727-95692777	ProgFib	skin:	n/a
24	chr2:95692727-95692777	CMK	blood:	n/a
25	chr2:95692727-95692777	RPTEC	kidney:	n/a
26	chr2:95692727-95692777	GM12892	blood:	n/a
27	chr2:95692727-95692777	AG04450	lung:	fetal
28	chr2:95692727-95692777	GM06990	blood:	n/a
29	chr2:95692727-95692777	HNPCEpiC	eye:	n/a
30	chr2:95692727-95692777	Jurkat	blood:	n/a
31	chr2:95692727-95692777	NT2-D1	testis:	n/a
32	chr2:95692727-95692777	GM12878	blood:	n/a
33	chr2:95692727-95692777	SK-N-SH	brain:	n/a
34	chr2:95692727-95692777	H1-hESC	embryonic stem cell:	embryo
35	chr2:95692727-95692777	HL-60	blood:	n/a
36	chr2:95692727-95692777	A549	lung:	n/a
37	chr2:95692727-95692777	HUVEC	blood vessel:	n/a
38	chr2:95692727-95692777	HRPEpiC	eye:	n/a
39	chr2:95692727-95692777	GM19239	blood:	n/a
40	chr2:95692727-95692777	NH-A	brain:	n/a
41	chr2:95692727-95692777	HIPEpiC	eye:	n/a
42	chr2:95692727-95692777	HAEpiC	amniotic membrane:	n/a
43	chr2:95692727-95692777	NHBE	bronchial:	n/a
44	chr2:95692727-95692777	AoSMC	blood vessel:	n/a
45	chr2:95692727-95692777	PANC-1	pancreas:	n/a
46	chr2:95692727-95692777	NB4	blood:	n/a
47	chr2:95692727-95692777	PrEC	prostate:	n/a
48	chr2:95692727-95692777	HepG2	liver:	n/a
49	chr2:95692727-95692777	AG09319	gingival:	n/a
50	chr2:95692727-95692777	AG04449	skin:	fetal

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95690048..95692826-chr2:95786470..95788667,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233850	TF binding region
ENSG00000233850	CpG island
ENSG00000144029	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1875402	0.82[CHB][hapmap]
rs3105098	0.91[CHB][hapmap]
rs3105099	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap]
rs3112982	0.82[CHB][hapmap]
rs3112983	0.82[CHB][hapmap]
rs3112985	0.81[CHB][hapmap]
rs3113002	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs4241315	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs7565772	0.91[CHB][hapmap]
rs7582368	0.91[CHB][hapmap]
rs872580	0.82[CHB][hapmap];0.86[CHD][hapmap]

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	nsv1000661	chr2:95327875-95739468	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1003666	chr2:95618109-95772924	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7560571	CYP4F32P	cis	Esophagus Mucosa	GTEx
rs7560571	ZNF514	cis	Artery Aorta	GTEx
rs7560571	ZNF514	cis	cerebellum	SCAN
rs7560571	ZNF514	cis	multi-tissue	Pritchard

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95690200-95692800	Active TSS	Brain Substantia Nigra	brain
2	chr2:95690200-95693200	Active TSS	Brain Anterior Caudate	brain
3	chr2:95690200-95693400	Active TSS	Brain Angular Gyrus	brain
4	chr2:95690200-95693600	Active TSS	Brain Cingulate Gyrus	brain
5	chr2:95690400-95692800	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr2:95690400-95694200	Active TSS	Thymus	Thymus
7	chr2:95690600-95692800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:95690600-95692800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr2:95690600-95693000	Active TSS	Right Atrium	heart
10	chr2:95690600-95693200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr2:95690600-95693400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr2:95690600-95693400	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr2:95690600-95693800	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr2:95690800-95692800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:95690800-95692800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:95690800-95692800	Bivalent/Poised TSS	GM12878-XiMat	blood
17	chr2:95690800-95693000	Bivalent Enhancer	Liver	Liver
18	chr2:95690800-95693000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
19	chr2:95690800-95693400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
20	chr2:95690800-95693800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr2:95691000-95693000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:95691000-95693000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:95691000-95693000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:95691000-95693200	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
25	chr2:95691600-95692800	Bivalent Enhancer	Fetal Intestine Large	intestine
26	chr2:95691800-95692800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr2:95691800-95693400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:95692000-95692800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:95692000-95692800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:95692000-95692800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr2:95692000-95693000	Bivalent Enhancer	Fetal Intestine Small	intestine
32	chr2:95692000-95693000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr2:95692000-95693400	Enhancers	Gastric	stomach
34	chr2:95692200-95692800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:95692200-95692800	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr2:95692200-95693200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr2:95692200-95693400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
38	chr2:95692200-95693400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:95692200-95693400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr2:95692400-95692800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:95692400-95692800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
42	chr2:95692400-95692800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:95692400-95692800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:95692400-95692800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:95692400-95692800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
46	chr2:95692400-95692800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
47	chr2:95692400-95692800	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
48	chr2:95692400-95693200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:95692400-95693200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
50	chr2:95692400-95693400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell

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