Variant report

Variant	rs838512
Chromosome Location	chr1:119874588-119874589
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	HDAC2	chr1:119874545-119874946	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:119874537-119875250	H1-hESC	embryonic stem cell:	n/a	chr1:119874936-119874944
3	TCF12	chr1:119874546-119874832	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr1:119874070-119875168	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:119874569..119876262-chr1:119880980..119883218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227712	TF binding region
RNU1-75P	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10802089	0.82[EUR][1000 genomes]
rs1409056	0.81[AMR][1000 genomes]
rs1891224	0.82[EUR][1000 genomes]
rs2153738	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2226102	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2243981	0.82[EUR][1000 genomes]
rs2253988	0.82[EUR][1000 genomes]
rs2254528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2254664	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2257016	0.82[EUR][1000 genomes]
rs2265628	0.82[EUR][1000 genomes]
rs2265629	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265630	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477889	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2477890	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6672571	0.82[EUR][1000 genomes]
rs6694847	1.00[MEX][hapmap]
rs699771	1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs838513	0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs838514	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs838515	0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs838516	0.94[ASW][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs838517	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838519	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838520	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838523	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs838524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs838525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs838526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs838527	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs838537	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs838538	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs866788	0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs947422	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs947423	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs947424	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs947425	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv547615	chr1:119828542-119875730	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised 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	41 gene(s)	inside rSNPs	diseases
7	esv2761649	chr1:119840645-119925936	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119870600-119874600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:119870600-119874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:119870600-119874800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:119870600-119874800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:119870600-119874800	Weak transcription	Esophagus	oesophagus
6	chr1:119870600-119875200	Enhancers	Fetal Muscle Leg	muscle
7	chr1:119870600-119879600	Weak transcription	Fetal Lung	lung
8	chr1:119870600-119879800	Weak transcription	Right Atrium	heart
9	chr1:119870800-119874600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:119870800-119874600	Weak transcription	GM12878-XiMat	blood
11	chr1:119870800-119883400	Weak transcription	Fetal Intestine Small	intestine
12	chr1:119871600-119874800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:119871600-119875000	Enhancers	Liver	Liver
14	chr1:119871600-119875000	Weak transcription	Fetal Kidney	kidney
15	chr1:119871800-119878000	Weak transcription	HepG2	liver
16	chr1:119872400-119874600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:119872400-119874600	Weak transcription	Placenta	Placenta
18	chr1:119872600-119875200	Weak transcription	Fetal Stomach	stomach
19	chr1:119872800-119876400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:119873400-119876000	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:119873800-119875400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr1:119873800-119876200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:119873800-119879200	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:119874000-119874600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr1:119874000-119875200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:119874000-119875800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:119874000-119876000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:119874200-119874600	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:119874200-119875400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:119874200-119875400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:119874200-119876400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr1:119874400-119874600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:119874400-119874800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:119874400-119874800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr1:119874400-119875600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:119874400-119876000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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