Variant report

Variant	rs12079115
Chromosome Location	chr1:120308275-120308276
allele	C/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	FOXA1	chr1:120308200-120308642	HepG2	liver:	n/a	n/a
2	FOXA2	chr1:120308018-120309794	HepG2	liver:	n/a	chr1:120309152-120309164
3	FOXA1	chr1:120308273-120308699	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:120307608..120310232-chr1:120312392..120315286,2	MCF-7	breast:
2	chr1:120300614..120303588-chr1:120307182..120308766,2	MCF-7	breast:
3	chr1:120305431..120308946-chr1:120308988..120311839,5	K562	blood:
4	chr1:120306158..120308946-chr1:120309949..120314499,4	K562	blood:

Variant related genes	Relation type
HMGCS2	TF binding region
ENSG00000134240	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10923897	1.00[CEU][hapmap];0.90[GIH][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11487674	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12070041	1.00[CEU][hapmap]
rs12070819	0.82[JPT][hapmap]
rs12406668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236399	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2236400	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2241868	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9943291	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised 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	20 gene(s)	inside rSNPs	diseases
6	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
2	chr1:120287200-120308800	Weak transcription	Fetal Kidney	kidney
3	chr1:120291000-120310600	Weak transcription	Placenta	Placenta
4	chr1:120298200-120312200	Weak transcription	Right Ventricle	heart
5	chr1:120301000-120311600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:120302600-120308400	Weak transcription	Colonic Mucosa	Colon
7	chr1:120302600-120308400	Weak transcription	Fetal Intestine Small	intestine
8	chr1:120307000-120308400	Enhancers	HepG2	liver
9	chr1:120307200-120308400	Weak transcription	Fetal Intestine Large	intestine
10	chr1:120307200-120308600	Weak transcription	Fetal Heart	heart
11	chr1:120307200-120308800	Weak transcription	Fetal Stomach	stomach
12	chr1:120307200-120308800	Weak transcription	Left Ventricle	heart
13	chr1:120307200-120309000	Weak transcription	Esophagus	oesophagus
14	chr1:120307200-120309200	Weak transcription	Gastric	stomach
15	chr1:120307200-120309600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:120307200-120312000	Active TSS	Duodenum Mucosa	Duodenum
17	chr1:120307400-120308600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:120307600-120308400	Active TSS	Liver	Liver
19	chr1:120307600-120308400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:120308000-120308400	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr1:120308200-120309800	Enhancers	Stomach Mucosa	stomach
22	chr1:120308200-120311600	Active TSS	Rectal Smooth Muscle	rectum

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