Variant report

Variant	rs16987945
Chromosome Location	chr2:20841721-20841722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr2:20841167-20842673	Hela-S3	cervix:	n/a	chr2:20842109-20842117 chr2:20842329-20842343 chr2:20842329-20842339 chr2:20842110-20842120
2	SMC3	chr2:20840332-20842911	SK-N-SH	brain:	n/a	chr2:20842109-20842117 chr2:20842710-20842720 chr2:20842329-20842343 chr2:20842329-20842339 chr2:20842110-20842120
3	POLR2A	chr2:20841472-20841735	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20602418..20604993-chr2:20841116..20842871,2	K562	blood:
2	chr2:20642724..20643586-chr2:20841568..20842737,5	MCF-7	breast:
3	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
4	chr2:20834621..20842195-chr2:20845758..20852616,8	MCF-7	breast:
5	chr2:20595167..20596377-chr2:20841669..20842665,4	MCF-7	breast:
6	chr2:20834987..20839141-chr2:20839755..20847316,8	K562	blood:
7	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
8	chr2:20584280..20586232-chr2:20840888..20843722,2	K562	blood:
9	chr2:20841431..20846177-chr2:20846336..20851141,14	MCF-7	breast:
10	chr2:20841385..20842959-chr2:20847975..20849536,2	K562	blood:
11	chr2:20839547..20841831-chr2:20843514..20846128,3	K562	blood:

Variant related genes	Relation type
HS1BP3	TF binding region
ENSG00000118960	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000232800	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs4426492	0.95[ASN][1000 genomes]
rs55766730	0.95[ASN][1000 genomes]
rs60631754	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62122090	0.95[ASN][1000 genomes]
rs62122091	0.95[ASN][1000 genomes]
rs62125672	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62125673	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62125674	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62125675	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62125676	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62125677	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6708069	0.85[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72784303	0.95[ASN][1000 genomes]
rs73916930	0.95[ASN][1000 genomes]
rs73916931	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
7	nsv999269	chr2:20824833-20869372	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
8	nsv873726	chr2:20829962-20876260	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	nsv873727	chr2:20838318-20876260	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:20820600-20849400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:20820800-20849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:20823000-20842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:20828600-20841800	Strong transcription	Primary T cells from cord blood	blood
11	chr2:20828800-20847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:20832600-20850000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:20833000-20841800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:20833800-20842000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:20833800-20843000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:20834400-20842000	Weak transcription	Fetal Thymus	thymus
17	chr2:20834800-20841800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:20834800-20849600	Weak transcription	Small Intestine	intestine
19	chr2:20835400-20849800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:20835600-20842000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:20835600-20847400	Weak transcription	HSMMtube	muscle
22	chr2:20835600-20847600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:20835600-20848800	Weak transcription	Fetal Lung	lung
24	chr2:20835600-20849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:20835600-20849800	Weak transcription	Fetal Heart	heart
26	chr2:20835800-20843000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:20836000-20841800	Strong transcription	Fetal Intestine Large	intestine
28	chr2:20836000-20841800	Strong transcription	Placenta	Placenta
29	chr2:20836000-20841800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:20836000-20841800	Weak transcription	HMEC	breast
31	chr2:20836000-20842000	Strong transcription	Fetal Intestine Small	intestine
32	chr2:20836000-20847400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:20836000-20847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:20836000-20850000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:20836200-20841800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:20836200-20841800	Weak transcription	Fetal Brain Male	brain
37	chr2:20836200-20842400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:20836200-20846400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:20836600-20845600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr2:20836800-20842000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:20837000-20841800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:20837000-20842800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
43	chr2:20837200-20841800	Strong transcription	Colonic Mucosa	Colon
44	chr2:20837200-20841800	Strong transcription	Pancreas	Pancrea
45	chr2:20837200-20842000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr2:20837400-20841800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:20837400-20841800	Weak transcription	Stomach Mucosa	stomach
48	chr2:20838400-20841800	Strong transcription	Gastric	stomach
49	chr2:20838600-20841800	Weak transcription	Right Atrium	heart
50	chr2:20838800-20841800	Strong transcription	HepG2	liver

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