Variant report

Variant	rs2288005
Chromosome Location	chr16:31227908-31227909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr16:31227855-31228660	H1-hESC	embryonic stem cell:	n/a	chr16:31228554-31228561 chr16:31228547-31228564 chr16:31228550-31228561 chr16:31228422-31228432 chr16:31228553-31228562
2	BACH1	chr16:31227815-31228368	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr16:31227888-31228618	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr16:31226988-31228222	H1-neurons	neurons:	n/a	n/a
5	E2F6	chr16:31227876-31228515	H1-hESC	embryonic stem cell:	n/a	chr16:31228422-31228432
6	MAX	chr16:31227900-31228546	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:31227884-31227934	HCF	heart:	n/a
2	chr16:31227884-31227934	AG04450	lung:	fetal
3	chr16:31227884-31227934	HRPEpiC	eye:	n/a
4	chr16:31227884-31227934	AG09319	gingival:	n/a
5	chr16:31227884-31227934	PrEC	prostate:	n/a
6	chr16:31227884-31227934	GM06990	blood:	n/a
7	chr16:31227884-31227934	HepG2	liver:	n/a
8	chr16:31227884-31227934	H1-hESC	embryonic stem cell:	embryo
9	chr16:31227884-31227934	AG10803	skin:	n/a
10	chr16:31227884-31227934	HL-60	blood:	n/a
11	chr16:31227884-31227934	NHBE	bronchial:	n/a
12	chr16:31227884-31227934	CMK	blood:	n/a
13	chr16:31227884-31227934	SAEC	small airway:	n/a
14	chr16:31227884-31227934	Jurkat	blood:	n/a
15	chr16:31227884-31227934	BE2_C	brain:	n/a
16	chr16:31227884-31227934	Hepatocyte	liver:	n/a
17	chr16:31227884-31227934	T-47D	breast:	n/a
18	chr16:31227884-31227934	ECC-1	luminal epithelium:	n/a
19	chr16:31227884-31227934	ovcar-3	ovarian:	n/a
20	chr16:31227884-31227934	GM12892	blood:	n/a
21	chr16:31227884-31227934	K562	blood:	n/a
22	chr16:31227884-31227934	Caco-2	colon:	n/a
23	chr16:31227884-31227934	HCPEpiC	choroid plexus:	n/a
24	chr16:31227884-31227934	IMR90	lung:	fetal
25	chr16:31227884-31227934	HCM	heart:	n/a
26	chr16:31227884-31227934	Hela-S3	cervix:	n/a
27	chr16:31227884-31227934	BJ	skin:	n/a
28	chr16:31227884-31227934	NH-A	brain:	n/a
29	chr16:31227884-31227934	HIPEpiC	eye:	n/a
30	chr16:31227884-31227934	HUVEC	blood vessel:	n/a
31	chr16:31227884-31227934	HMEC	breast:	n/a
32	chr16:31227884-31227934	HEK293	kidney:	embryo
33	chr16:31227884-31227934	AoSMC	blood vessel:	n/a
34	chr16:31227884-31227934	SK-N-SH_RA	brain:	n/a
35	chr16:31227884-31227934	GM12878	blood:	n/a
36	chr16:31227884-31227934	HAEpiC	amniotic membrane:	n/a
37	chr16:31227884-31227934	A549	lung:	n/a
38	chr16:31227884-31227934	NT2-D1	testis:	n/a
39	chr16:31227884-31227934	PFSK-1	brain:	n/a
40	chr16:31227884-31227934	RPTEC	kidney:	n/a
41	chr16:31227884-31227934	SK-N-SH	brain:	n/a
42	chr16:31227884-31227934	MCF-7	breast:	n/a
43	chr16:31227884-31227934	HCT-116	colon:	n/a
44	chr16:31227884-31227934	ProgFib	skin:	n/a
45	chr16:31227884-31227934	AG04449	skin:	fetal
46	chr16:31227884-31227934	SK-N-MC	brain:	n/a
47	chr16:31227884-31227934	NB4	blood:	n/a
48	chr16:31227884-31227934	GM19239	blood:	n/a
49	chr16:31227884-31227934	NHDF-neo	bronchial:	n/a
50	chr16:31227884-31227934	HRE	kidney:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31145063..31147795-chr16:31225870..31228416,3	MCF-7	breast:
2	chr16:31190054..31194646-chr16:31224217..31229118,11	MCF-7	breast:
3	chr16:31225327..31230953-chr16:31277531..31282411,8	MCF-7	breast:
4	chr16:31189605..31193047-chr16:31225207..31229243,8	MCF-7	breast:
5	chr16:31225061..31229339-chr16:31234222..31239323,4	MCF-7	breast:
6	chr16:31225508..31229530-chr16:31277117..31281279,6	MCF-7	breast:
7	chr16:31104754..31107641-chr16:31225871..31228750,3	MCF-7	breast:
8	chr16:31127390..31129807-chr16:31225827..31228203,2	MCF-7	breast:

No data

Variant related genes	Relation type
PYDC1	TF binding region
PYDC1	CpG island
ENSG00000089280	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000052344	Chromatin interaction
ENSG00000252876	Chromatin interaction
ENSG00000167397	Chromatin interaction
ENSG00000261925	Chromatin interaction
ENSG00000103510	Chromatin interaction
ENSG00000260304	Chromatin interaction
ENSG00000255439	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1052352	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11641624	0.82[JPT][hapmap]
rs11645526	0.83[JPT][hapmap]
rs11864632	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12929077	0.85[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs13333997	0.87[ASN][1000 genomes]
rs17708638	0.82[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs2735393	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3764323	0.94[ASN][1000 genomes]
rs3764327	0.83[JPT][hapmap]
rs4496161	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889537	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4889538	0.96[ASN][1000 genomes]
rs4889623	0.84[CEU][hapmap]
rs4889633	0.94[ASN][1000 genomes]
rs4889640	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs57348955	0.90[ASN][1000 genomes]
rs7184910	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7186832	0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7187143	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7193943	0.83[JPT][hapmap]
rs741810	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8056505	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8057320	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer 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 lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
6	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
7	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription 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 target site	202 gene(s)	inside rSNPs	diseases
8	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases
9	nsv905744	chr16:31216517-31234288	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv905745	chr16:31216517-31247924	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv571823	chr16:31216909-31227908	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv1066073	chr16:31219071-31278572	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	nsv905746	chr16:31223549-31237920	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31225600-31228600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr16:31225800-31228000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr16:31226000-31228000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr16:31226000-31228200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr16:31226000-31228600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr16:31226000-31228600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
7	chr16:31226000-31228600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
8	chr16:31226200-31228400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
9	chr16:31226200-31228400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:31226200-31228400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
11	chr16:31226200-31228400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
12	chr16:31226200-31228600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
13	chr16:31226400-31228400	Bivalent Enhancer	Fetal Thymus	thymus
14	chr16:31226400-31228600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr16:31226400-31228600	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr16:31226600-31228600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
17	chr16:31226800-31228400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
18	chr16:31227000-31228000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:31227000-31228200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
20	chr16:31227000-31228400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr16:31227000-31228600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
22	chr16:31227000-31228600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr16:31227000-31228600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr16:31227000-31228600	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
25	chr16:31227000-31228600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
26	chr16:31227200-31228200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:31227200-31228400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
28	chr16:31227200-31228400	Bivalent Enhancer	Fetal Lung	lung
29	chr16:31227200-31228400	Enhancers	Lung	lung
30	chr16:31227200-31228600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr16:31227200-31228600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
32	chr16:31227200-31228600	Bivalent Enhancer	Placenta	Placenta
33	chr16:31227200-31228600	Enhancers	Ovary	ovary
34	chr16:31227400-31228000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr16:31227400-31228000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:31227400-31228000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr16:31227400-31228000	Bivalent Enhancer	Fetal Intestine Large	intestine
38	chr16:31227400-31228000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
39	chr16:31227400-31228200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr16:31227400-31228200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr16:31227400-31228400	Bivalent Enhancer	Fetal Brain Male	brain
42	chr16:31227400-31228400	Bivalent Enhancer	NHEK	skin
43	chr16:31227400-31228600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr16:31227400-31228600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr16:31227400-31228600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr16:31227400-31228600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
47	chr16:31227400-31228600	Bivalent Enhancer	Fetal Stomach	stomach
48	chr16:31227400-31228600	Enhancers	Pancreas	Pancrea
49	chr16:31227400-31228800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr16:31227600-31228000	Bivalent Enhancer	Primary B cells from cord blood	blood

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