Variant report

Variant	rs11204846
Chromosome Location	chr1:151516080-151516081
allele	A/G
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	chr1:151515840-151516586	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151481429..151491154-chr1:151502501..151517487,49	MCF-7	breast:
2	chr1:151481542..151488437-chr1:151515636..151525415,14	MCF-7	breast:
3	chr1:151515446..151517713-chr1:151630494..151632395,2	MCF-7	breast:
4	chr1:151514211..151516187-chr1:151541825..151543936,2	MCF-7	breast:

Variant related genes	Relation type
MIR554	TF binding region
ENSG00000143375	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10158855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034149	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12117155	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12753658	0.95[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1891593	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2337360	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34589182	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35436273	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3828054	1.00[JPT][hapmap]
rs3828055	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4970956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4970958	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56096667	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56188938	0.84[EUR][1000 genomes]
rs6669998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7521397	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7526319	0.87[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7549296	1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868138	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151513800-151519400	Weak transcription	Left Ventricle	heart
2	chr1:151514000-151516200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:151514000-151519400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:151514000-151519400	Weak transcription	HUVEC	blood vessel
5	chr1:151514200-151516200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:151514200-151516200	Flanking Active TSS	HSMMtube	muscle
7	chr1:151514200-151517800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:151514200-151519400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:151514200-151519400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:151514200-151519400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:151514200-151519600	Weak transcription	Fetal Heart	heart
12	chr1:151514200-151519600	Weak transcription	Ovary	ovary
13	chr1:151514400-151516200	Enhancers	Adipose Nuclei	Adipose
14	chr1:151514400-151519400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:151514400-151519600	Weak transcription	Psoas Muscle	Psoas
16	chr1:151514400-151519800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:151514400-151540800	Weak transcription	Brain Angular Gyrus	brain
18	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
19	chr1:151514600-151516200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:151514600-151516200	Enhancers	NHDF-Ad	bronchial
21	chr1:151514600-151516400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:151514600-151516400	Enhancers	Pancreas	Pancrea
23	chr1:151514600-151516600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:151514600-151519200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:151514600-151519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:151514600-151519400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:151514600-151519400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:151514600-151519600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:151514600-151519800	Weak transcription	Fetal Stomach	stomach
30	chr1:151514800-151519200	Weak transcription	Liver	Liver
31	chr1:151515400-151516600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:151515400-151518000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:151515400-151519400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:151515400-151519400	Weak transcription	Small Intestine	intestine
35	chr1:151515400-151519400	Weak transcription	Stomach Mucosa	stomach
36	chr1:151515400-151519600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:151515400-151523400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:151515600-151516200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:151515600-151516400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr1:151515600-151516400	Flanking Active TSS	NHEK	skin
41	chr1:151515600-151516400	Enhancers	NHLF	lung
42	chr1:151515600-151516600	Enhancers	Fetal Intestine Large	intestine
43	chr1:151515600-151517600	Weak transcription	Placenta	Placenta
44	chr1:151515600-151518200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:151515600-151518200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:151515600-151519000	Weak transcription	HepG2	liver
47	chr1:151515600-151519200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:151515600-151519400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:151515600-151519400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:151515600-151519400	Weak transcription	Esophagus	oesophagus

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