Variant report

Variant	rs12123085
Chromosome Location	chr1:120309593-120309594
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	CEBPZ	chr1:120309578-120309646	HepG2	liver:	n/a	n/a
2	FOXA2	chr1:120308018-120309794	HepG2	liver:	n/a	chr1:120309152-120309164
3	MAZ	chr1:120309592-120309651	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:120307608..120310232-chr1:120312392..120315286,2	MCF-7	breast:
2	chr1:120302494..120304014-chr1:120308491..120310237,2	K562	blood:
3	chr1:120305431..120308946-chr1:120308988..120311839,5	K562	blood:

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1163542	0.86[ASN][1000 genomes]
rs1163550	0.86[ASN][1000 genomes]
rs1177389	0.86[ASN][1000 genomes]
rs12121219	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12132674	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1660607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17024167	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17186233	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17258425	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1814447	0.86[ASN][1000 genomes]
rs2582784	1.00[JPT][hapmap]
rs2582786	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2843014	0.86[ASN][1000 genomes]
rs2843016	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2843017	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4391705	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs4659019	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs4659233	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs56239558	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753425	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs930448	1.00[JPT][hapmap];0.86[ASN][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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
2	chr1:120291000-120310600	Weak transcription	Placenta	Placenta
3	chr1:120298200-120312200	Weak transcription	Right Ventricle	heart
4	chr1:120301000-120311600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:120307200-120309600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:120307200-120312000	Active TSS	Duodenum Mucosa	Duodenum
7	chr1:120308200-120309800	Enhancers	Stomach Mucosa	stomach
8	chr1:120308200-120311600	Active TSS	Rectal Smooth Muscle	rectum
9	chr1:120308400-120309800	Enhancers	Adipose Nuclei	Adipose
10	chr1:120308400-120309800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:120308400-120310000	Enhancers	Brain Substantia Nigra	brain
12	chr1:120308400-120310000	Flanking Active TSS	Fetal Intestine Large	intestine
13	chr1:120308400-120310400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr1:120308400-120310600	Enhancers	Brain Hippocampus Middle	brain
15	chr1:120308400-120311800	Active TSS	Colonic Mucosa	Colon
16	chr1:120308600-120309600	Enhancers	Stomach Smooth Muscle	stomach
17	chr1:120308600-120309800	Enhancers	Brain Angular Gyrus	brain
18	chr1:120308600-120310200	Enhancers	Small Intestine	intestine
19	chr1:120308800-120309600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:120308800-120309800	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr1:120308800-120310000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:120308800-120310000	Enhancers	Colon Smooth Muscle	Colon
23	chr1:120308800-120310200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:120308800-120310200	Enhancers	Fetal Kidney	kidney
25	chr1:120308800-120310200	Flanking Active TSS	Fetal Stomach	stomach
26	chr1:120308800-120310200	Enhancers	Pancreas	Pancrea
27	chr1:120308800-120311200	Active TSS	Liver	Liver
28	chr1:120308800-120311800	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:120309000-120309600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:120309000-120309600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr1:120309000-120309800	Enhancers	Brain Anterior Caudate	brain
32	chr1:120309000-120309800	Enhancers	Ovary	ovary
33	chr1:120309000-120312000	Enhancers	Fetal Lung	lung
34	chr1:120309200-120309600	Weak transcription	Esophagus	oesophagus
35	chr1:120309200-120309800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:120309200-120310000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:120309200-120310000	Enhancers	Brain Cingulate Gyrus	brain
38	chr1:120309200-120310200	Enhancers	Gastric	stomach
39	chr1:120309200-120311400	Weak transcription	Fetal Heart	heart
40	chr1:120309400-120309600	Weak transcription	Left Ventricle	heart
41	chr1:120309400-120310200	Flanking Active TSS	HepG2	liver
42	chr1:120309400-120311400	Weak transcription	Right Atrium	heart
43	chr1:120309400-120311800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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