Variant report

Variant	rs4666445
Chromosome Location	chr2:20825365-20825366
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	FOXA1	chr2:20825291-20825835	HepG2	liver:	n/a	chr2:20825575-20825590
2	FOXA1	chr2:20825345-20825823	HepG2	liver:	n/a	chr2:20825575-20825590
3	FOXA1	chr2:20825313-20825807	HepG2	liver:	n/a	chr2:20825575-20825590
4	FOXA1	chr2:20825301-20825778	HepG2	liver:	n/a	chr2:20825575-20825590

No.	Distal block	Cell Line	Cell type
1	chr2:20798603..20801119-chr2:20825014..20826613,2	K562	blood:
2	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
3	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
4	chr2:20816763..20821100-chr2:20824834..20828532,5	K562	blood:
5	chr2:20818868..20821100-chr2:20824834..20827973,3	K562	blood:

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

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10186292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10186814	0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10187254	0.98[ASN][1000 genomes]
rs10191266	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199441	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10432583	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1047169	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs11096680	0.83[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs11687806	0.98[ASN][1000 genomes]
rs12468175	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12476211	0.99[ASN][1000 genomes]
rs12710742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12998196	1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[ASN][1000 genomes]
rs13022516	0.83[ASN][1000 genomes]
rs1344836	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs1529896	0.82[ASN][1000 genomes]
rs1865678	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2033639	0.98[ASN][1000 genomes]
rs2033640	0.96[ASN][1000 genomes]
rs2305457	0.83[MEX][hapmap]
rs3732151	0.89[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs3796064	0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4402715	0.98[ASN][1000 genomes]
rs4666318	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4666438	0.83[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4666439	1.00[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4666446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4666447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4666449	0.90[CHB][hapmap]
rs60569709	0.99[ASN][1000 genomes]
rs62122089	0.83[ASN][1000 genomes]
rs6737130	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6750073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7423811	0.98[ASN][1000 genomes]
rs875672	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[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	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	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
3	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20817200-20826600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:20817400-20827200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:20817800-20826200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
12	chr2:20818000-20825600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:20818200-20828600	Weak transcription	Fetal Kidney	kidney
14	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:20818400-20825600	Weak transcription	HUVEC	blood vessel
17	chr2:20818400-20828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:20818400-20828800	Weak transcription	Fetal Brain Male	brain
19	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:20818600-20825600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:20818800-20826200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
22	chr2:20818800-20833600	Weak transcription	A549	lung
23	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:20819200-20825400	Strong transcription	Primary B cells from cord blood	blood
26	chr2:20819200-20826200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:20819200-20827000	Strong transcription	Primary T cells from cord blood	blood
28	chr2:20819200-20827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:20819400-20825600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:20819600-20825600	Strong transcription	Pancreas	Pancrea
33	chr2:20819800-20826400	Strong transcription	Aorta	Aorta
34	chr2:20819800-20826800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:20819800-20834200	Weak transcription	Osteobl	bone
36	chr2:20820600-20826000	Strong transcription	Fetal Stomach	stomach
37	chr2:20820600-20827000	Genic enhancers	Right Ventricle	heart
38	chr2:20820600-20827200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:20820600-20849400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:20820800-20826400	Genic enhancers	Stomach Smooth Muscle	stomach
41	chr2:20820800-20849600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:20821000-20826800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:20821400-20831800	Weak transcription	NHEK	skin
44	chr2:20821600-20826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:20821800-20825400	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr2:20822000-20832600	Weak transcription	Hela-S3	cervix
47	chr2:20822200-20828800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:20822400-20826600	Strong transcription	Placenta	Placenta
49	chr2:20822600-20826200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:20823000-20833600	Weak transcription	Muscle Satellite Cultured Cells	--

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