Variant report

Variant	rs12042509
Chromosome Location	chr1:94798658-94798659
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	SPI1	chr1:94797948-94798766	GM12878	blood:	n/a	chr1:94798252-94798261
2	FOSL2	chr1:94798435-94799023	SK-N-SH	brain:	n/a	chr1:94798712-94798721 chr1:94798711-94798722 chr1:94798713-94798724
3	EP300	chr1:94798646-94798904	GM12878	blood:	n/a	chr1:94798793-94798807
4	FOSL2	chr1:94798533-94798847	HepG2	liver:	n/a	chr1:94798712-94798721 chr1:94798711-94798722 chr1:94798713-94798724
5	BHLHE40	chr1:94798658-94798814	GM12878	blood:	n/a	n/a
6	NFIC	chr1:94798416-94798934	GM12878	blood:	n/a	n/a
7	FOS	chr1:94798544-94798847	MCF10A-Er-Src	breast:	n/a	chr1:94798712-94798721 chr1:94798713-94798724
8	JUND	chr1:94798564-94798896	HepG2	liver:	n/a	chr1:94798710-94798721 chr1:94798712-94798721 chr1:94798713-94798724
9	PBX3	chr1:94798401-94798879	SK-N-SH	brain:	n/a	n/a
10	FOSL2	chr1:94798476-94798939	HepG2	liver:	n/a	chr1:94798712-94798721 chr1:94798711-94798722 chr1:94798713-94798724
11	SRF	chr1:94798193-94798920	ECC-1	luminal epithelium:	n/a	n/a
12	MYC	chr1:94798513-94798713	MCF10A-Er-Src	breast:	n/a	n/a
13	SRF	chr1:94798619-94798818	GM12878	blood:	n/a	n/a
14	FOS	chr1:94798605-94798799	MCF10A-Er-Src	breast:	n/a	chr1:94798712-94798721 chr1:94798713-94798724
15	FOS	chr1:94798600-94798808	MCF10A-Er-Src	breast:	n/a	chr1:94798712-94798721 chr1:94798713-94798724
16	EP300	chr1:94798162-94799200	ECC-1	luminal epithelium:	n/a	chr1:94798793-94798807 chr1:94798247-94798261
17	PBX3	chr1:94798382-94798917	SK-N-SH	brain:	n/a	n/a
18	FOXM1	chr1:94798495-94798894	GM12878	blood:	n/a	n/a
19	MXI1	chr1:94798647-94798674	GM12878	blood:	n/a	n/a
20	FOS	chr1:94798553-94798846	MCF10A-Er-Src	breast:	n/a	chr1:94798712-94798721 chr1:94798713-94798724
21	RUNX3	chr1:94798460-94798884	GM12878	blood:	n/a	n/a
22	RAD21	chr1:94798590-94798861	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94524835..94527724-chr1:94798552..94800345,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226835	TF binding region
ENSG00000198691	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1054626	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11165103	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11165114	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs12024941	0.95[EUR][1000 genomes]
rs12027548	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12031606	0.95[EUR][1000 genomes]
rs12036085	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12038745	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12039546	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12046536	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs12093742	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12562103	1.00[EUR][1000 genomes]
rs12563826	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1360365	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1576592	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1611832	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1622451	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1623248	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1623314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1629275	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1687947	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1687950	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111408	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17111419	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17111426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17111436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1765636	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1765640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1929131	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1999270	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs1999271	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs2130899	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2391472	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35275815	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3789690	0.83[EUR][1000 genomes]
rs4543802	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847201	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs4847296	0.90[EUR][1000 genomes]
rs55961421	0.92[EUR][1000 genomes]
rs56037795	0.95[EUR][1000 genomes]
rs57666908	0.83[EUR][1000 genomes]
rs6541343	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs6541345	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6662877	0.98[EUR][1000 genomes]
rs6673491	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs6675959	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs6681827	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs66918029	0.92[EUR][1000 genomes]
rs66961454	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67180557	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67554381	0.94[EUR][1000 genomes]
rs67612304	1.00[EUR][1000 genomes]
rs67681803	0.95[EUR][1000 genomes]
rs67807923	0.98[EUR][1000 genomes]
rs68193246	1.00[EUR][1000 genomes]
rs7413345	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7415246	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7515965	0.91[EUR][1000 genomes]
rs7520754	0.90[EUR][1000 genomes]
rs7525320	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7533977	0.91[EUR][1000 genomes]
rs7554714	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][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	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94788600-94800800	Weak transcription	Pancreas	Pancrea
2	chr1:94790800-94799200	Enhancers	Fetal Heart	heart
3	chr1:94792400-94800200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:94793000-94798800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:94793200-94800600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:94793400-94798800	Weak transcription	Placenta	Placenta
7	chr1:94796000-94798800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:94796000-94798800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:94796000-94800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:94796000-94800200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:94796000-94800400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:94796000-94800600	Weak transcription	Adipose Nuclei	Adipose
13	chr1:94796000-94800600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:94796000-94804600	Weak transcription	Fetal Thymus	thymus
15	chr1:94796000-94804800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:94796000-94807800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:94796200-94799800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:94796200-94800400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:94796400-94800200	Weak transcription	Left Ventricle	heart
20	chr1:94796600-94798800	Weak transcription	Fetal Stomach	stomach
21	chr1:94796600-94804800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:94797400-94798800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:94798200-94799000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:94798200-94799000	Enhancers	NHDF-Ad	bronchial
25	chr1:94798200-94799400	Enhancers	NH-A	brain
26	chr1:94798200-94801400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:94798200-94802000	Enhancers	Osteobl	bone
28	chr1:94798200-94802400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:94798400-94799000	Enhancers	Fetal Kidney	kidney
30	chr1:94798400-94799000	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr1:94798400-94799000	Flanking Active TSS	GM12878-XiMat	blood
32	chr1:94798400-94799000	Enhancers	HUVEC	blood vessel
33	chr1:94798400-94799200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:94798400-94799200	Enhancers	NHEK	skin
35	chr1:94798400-94799600	Enhancers	HepG2	liver
36	chr1:94798400-94801000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:94798400-94801000	Enhancers	HSMMtube	muscle
38	chr1:94798400-94801200	Enhancers	A549	lung
39	chr1:94798400-94801200	Enhancers	HSMM	muscle
40	chr1:94798400-94801400	Enhancers	HMEC	breast
41	chr1:94798600-94798800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:94798600-94799000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:94798600-94799000	Enhancers	Lung	lung
44	chr1:94798600-94799200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:94798600-94799200	Enhancers	Fetal Muscle Leg	muscle
46	chr1:94798600-94799200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr1:94798600-94799400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:94798600-94800200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:94798600-94801200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:94798600-94801200	Enhancers	NHLF	lung

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