Variant report

Variant	rs4666439
Chromosome Location	chr2:20810659-20810660
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	MAX	chr2:20810410-20812157	HepG2	liver:	n/a	chr2:20811266-20811275
2	MAX	chr2:20810545-20811768	HepG2	liver:	n/a	chr2:20811266-20811275
3	POLR2A	chr2:20810510-20811771	HepG2	liver:	n/a	n/a
4	MBD4	chr2:20810557-20811569	HepG2	liver:	n/a	n/a
5	FOXA2	chr2:20810313-20811714	HepG2	liver:	n/a	n/a
6	TEAD4	chr2:20810642-20812020	HepG2	liver:	n/a	n/a
7	MYBL2	chr2:20810309-20812046	HepG2	liver:	n/a	n/a
8	NFIC	chr2:20810642-20811668	HepG2	liver:	n/a	n/a
9	MYBL2	chr2:20810251-20811986	HepG2	liver:	n/a	n/a
10	MBD4	chr2:20810558-20811556	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20807683..20810867-chr2:20811760..20818347,7	MCF-7	breast:
2	chr2:20810389..20812991-chr2:20823775..20826259,2	MCF-7	breast:
3	chr2:20807940..20810895-chr2:20811294..20813861,2	K562	blood:

Variant related genes	Relation type
ENSG00000233416	TF binding region
ENSG00000118960	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10186292	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10186814	0.84[ASN][1000 genomes]
rs10187254	0.84[ASN][1000 genomes]
rs10191266	1.00[CEU][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10199441	0.91[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs1047169	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11096680	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11687806	0.84[ASN][1000 genomes]
rs12468175	0.88[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12476211	0.85[ASN][1000 genomes]
rs12710742	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12998196	0.89[CHD][hapmap];0.84[MEX][hapmap]
rs1529896	0.96[ASN][1000 genomes]
rs1865678	0.84[GIH][hapmap]
rs2033639	0.84[ASN][1000 genomes]
rs2033640	0.82[ASN][1000 genomes]
rs3732151	0.81[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3796064	0.84[GIH][hapmap]
rs4402715	0.84[ASN][1000 genomes]
rs4666318	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4666438	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4666445	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	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4666447	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs60569709	0.85[ASN][1000 genomes]
rs6737130	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6750073	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7423811	0.84[ASN][1000 genomes]
rs875672	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20797800-20810800	Weak transcription	Gastric	stomach
2	chr2:20803200-20814000	Weak transcription	HSMM	muscle
3	chr2:20804400-20813400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:20805200-20813600	Weak transcription	HMEC	breast
5	chr2:20805200-20813800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:20805200-20814000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:20805200-20816000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:20808400-20811800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:20808400-20811800	Enhancers	Fetal Intestine Large	intestine
10	chr2:20808400-20811800	Enhancers	Fetal Muscle Trunk	muscle
11	chr2:20808400-20813600	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:20808400-20814200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:20808400-20816400	Enhancers	Rectal Smooth Muscle	rectum
14	chr2:20808400-20816600	Enhancers	Colon Smooth Muscle	Colon
15	chr2:20808400-20816800	Enhancers	Adipose Nuclei	Adipose
16	chr2:20808400-20819600	Enhancers	Fetal Muscle Leg	muscle
17	chr2:20808600-20811800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:20808600-20812000	Enhancers	Fetal Stomach	stomach
19	chr2:20808600-20812000	Enhancers	Left Ventricle	heart
20	chr2:20808600-20812000	Enhancers	Right Atrium	heart
21	chr2:20808600-20812000	Enhancers	Right Ventricle	heart
22	chr2:20808600-20812000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr2:20808600-20812400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr2:20808600-20818600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr2:20808600-20819400	Enhancers	Brain Anterior Caudate	brain
26	chr2:20808600-20819800	Enhancers	Brain Substantia Nigra	brain
27	chr2:20808800-20811800	Enhancers	NHLF	lung
28	chr2:20808800-20812000	Enhancers	Ovary	ovary
29	chr2:20809000-20817200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:20809200-20811600	Enhancers	K562	blood
31	chr2:20809200-20811800	Enhancers	Liver	Liver
32	chr2:20809200-20811800	Enhancers	Fetal Intestine Small	intestine
33	chr2:20809200-20812000	Enhancers	Stomach Mucosa	stomach
34	chr2:20809200-20813000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:20809400-20810800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:20809400-20811400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:20809400-20816200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr2:20809600-20810800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:20809600-20810800	Weak transcription	Placenta	Placenta
40	chr2:20809600-20811000	Enhancers	Stomach Smooth Muscle	stomach
41	chr2:20809600-20811200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:20809600-20812600	Weak transcription	Fetal Brain Female	brain
43	chr2:20809600-20813000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:20809600-20813400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:20809600-20813600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:20809600-20813800	Weak transcription	NHEK	skin
47	chr2:20809600-20814000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:20809600-20814200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:20809600-20814200	Weak transcription	Brain Germinal Matrix	brain
50	chr2:20809600-20816600	Weak transcription	Fetal Thymus	thymus

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