Variant report

Variant	rs7268237
Chromosome Location	chr20:25652197-25652198
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	POLR2A	chr20:25652171-25652574	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr20:25652195-25652360	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25604700..25606724-chr20:25650561..25652560,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GINS1-5	chr20:25651389-25652886	NONHSAT079176

Variant related genes	Relation type
MED28P7	TF binding region
ENSG00000213742	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1119163	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13040726	1.00[CHB][hapmap]
rs1985401	0.85[AMR][1000 genomes]
rs1985402	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1985403	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009090	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2387976	1.00[CHB][hapmap]
rs2890396	0.91[EUR][1000 genomes]
rs3752273	1.00[CHB][hapmap]
rs4597609	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4813575	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815440	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4815447	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57199512	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6037158	1.00[CHB][hapmap]
rs6037225	0.91[EUR][1000 genomes]
rs6037229	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6037230	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050859	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6050941	1.00[CHB][hapmap];0.80[GIH][hapmap];0.94[MEX][hapmap]
rs6107051	1.00[ASN][1000 genomes]
rs6107060	1.00[CHB][hapmap]
rs6107062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107072	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115190	1.00[ASN][1000 genomes]
rs6115230	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115239	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115240	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115244	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6115261	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115262	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115270	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115272	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115273	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115275	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6115350	1.00[CHB][hapmap]
rs6115355	1.00[CHB][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap]
rs61672495	1.00[ASN][1000 genomes]
rs6515674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7268489	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7273102	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7273313	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7274511	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7274637	0.84[EUR][1000 genomes]
rs8118180	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8123585	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs958075	1.00[CHB][hapmap]
rs9808606	1.00[ASN][1000 genomes]
rs9917437	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912834	chr20:25615272-25756336	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25605600-25654600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:25609200-25653400	Weak transcription	Brain Substantia Nigra	brain
3	chr20:25611400-25653200	Weak transcription	Fetal Intestine Small	intestine
4	chr20:25616000-25653600	Weak transcription	Adipose Nuclei	Adipose
5	chr20:25617600-25653400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr20:25618400-25653600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr20:25618400-25653600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr20:25623200-25653600	Weak transcription	Pancreas	Pancrea
9	chr20:25625000-25655200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr20:25626400-25653600	Weak transcription	Fetal Muscle Leg	muscle
11	chr20:25626800-25654000	Weak transcription	Gastric	stomach
12	chr20:25628200-25653600	Weak transcription	Esophagus	oesophagus
13	chr20:25628800-25653400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr20:25628800-25653400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr20:25628800-25653400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr20:25629000-25652200	Weak transcription	Liver	Liver
17	chr20:25629000-25653400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr20:25629000-25653600	Weak transcription	Brain Hippocampus Middle	brain
19	chr20:25629000-25653600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr20:25629000-25653800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr20:25632600-25653600	Weak transcription	Brain Anterior Caudate	brain
22	chr20:25641200-25653800	Weak transcription	Right Ventricle	heart
23	chr20:25641600-25653800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr20:25642600-25653400	Weak transcription	Dnd41	blood
25	chr20:25642800-25652200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr20:25643400-25653400	Weak transcription	A549	lung
27	chr20:25648000-25653600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr20:25648000-25653800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:25648600-25653400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:25649200-25653200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr20:25649200-25655200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr20:25649400-25653600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr20:25649400-25653800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr20:25649400-25653800	Weak transcription	Spleen	Spleen
35	chr20:25649400-25654400	Weak transcription	Fetal Kidney	kidney
36	chr20:25649600-25653600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr20:25649600-25653600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr20:25649600-25654000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr20:25649800-25653400	Weak transcription	Thymus	Thymus
40	chr20:25650000-25652600	Enhancers	HepG2	liver
41	chr20:25650200-25652600	Weak transcription	Fetal Stomach	stomach
42	chr20:25650400-25652600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr20:25650400-25653600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr20:25650400-25653800	Weak transcription	Primary B cells from cord blood	blood
45	chr20:25650400-25653800	Weak transcription	K562	blood
46	chr20:25650600-25652200	Weak transcription	NH-A	brain
47	chr20:25650600-25653400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr20:25650600-25655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr20:25650600-25655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr20:25650600-25657000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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