Variant report

Variant	rs1441008
Chromosome Location	chr1:120310292-120310293
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	NFIC	chr1:120310161-120310551	SK-N-SH	brain:	n/a	chr1:120310368-120310384 chr1:120310368-120310385 chr1:120310369-120310386
2	JUND	chr1:120310085-120310410	HepG2	liver:	n/a	chr1:120310231-120310242 chr1:120310232-120310241 chr1:120310232-120310242
3	EP300	chr1:120310045-120310545	SK-N-SH_RA	brain:	n/a	n/a
4	FOS	chr1:120310099-120310368	MCF10A-Er-Src	breast:	n/a	chr1:120310232-120310241 chr1:120310232-120310242
5	FOS	chr1:120310172-120310391	MCF10A-Er-Src	breast:	n/a	chr1:120310232-120310241 chr1:120310232-120310242
6	EP300	chr1:120310056-120310483	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr1:120310106-120310454	PFSK-1	brain:	n/a	n/a
8	FOS	chr1:120310207-120310349	MCF10A-Er-Src	breast:	n/a	chr1:120310232-120310241 chr1:120310232-120310242

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120306158..120308946-chr1:120309949..120314499,4	K562	blood:
2	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: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12562383	0.95[CHB][hapmap];0.82[CHD][hapmap]
rs3790692	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3790693	0.90[CHB][hapmap]
rs3790694	0.91[CHB][hapmap]
rs3828089	0.90[CHB][hapmap]
rs522277	0.82[CHB][hapmap]
rs590825	0.82[CHB][hapmap]
rs591162	0.82[CHB][hapmap]
rs593911	0.82[CHB][hapmap]
rs608358	0.86[CHB][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs651347	0.82[CHB][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1441008	ILVBL	trans	parietal	SCAN
rs1441008	VANGL1	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120291000-120310600	Weak transcription	Placenta	Placenta
2	chr1:120298200-120312200	Weak transcription	Right Ventricle	heart
3	chr1:120301000-120311600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:120307200-120312000	Active TSS	Duodenum Mucosa	Duodenum
5	chr1:120308200-120311600	Active TSS	Rectal Smooth Muscle	rectum
6	chr1:120308400-120310400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:120308400-120310600	Enhancers	Brain Hippocampus Middle	brain
8	chr1:120308400-120311800	Active TSS	Colonic Mucosa	Colon
9	chr1:120308800-120311200	Active TSS	Liver	Liver
10	chr1:120308800-120311800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:120309000-120312000	Enhancers	Fetal Lung	lung
12	chr1:120309200-120311400	Weak transcription	Fetal Heart	heart
13	chr1:120309400-120311400	Weak transcription	Right Atrium	heart
14	chr1:120309400-120311800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:120309600-120310400	Enhancers	Esophagus	oesophagus
16	chr1:120309600-120310800	Enhancers	Left Ventricle	heart
17	chr1:120309600-120311400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:120309800-120310400	Enhancers	Lung	lung
19	chr1:120309800-120310800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:120309800-120311200	Weak transcription	Adipose Nuclei	Adipose
21	chr1:120309800-120311400	Weak transcription	Ovary	ovary
22	chr1:120309800-120311600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:120309800-120311600	Active TSS	Fetal Intestine Small	intestine
24	chr1:120309800-120313800	Weak transcription	Brain Anterior Caudate	brain
25	chr1:120309800-120316000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:120310000-120310400	Enhancers	Hela-S3	cervix
27	chr1:120310000-120311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:120310000-120311200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:120310000-120311400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:120310000-120311600	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr1:120310000-120316200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:120310000-120316600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:120310200-120310400	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr1:120310200-120310400	Flanking Active TSS	Fetal Kidney	kidney
35	chr1:120310200-120310800	Enhancers	Stomach Mucosa	stomach
36	chr1:120310200-120310800	Enhancers	HepG2	liver
37	chr1:120310200-120311200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:120310200-120311400	Weak transcription	Gastric	stomach
39	chr1:120310200-120311400	Weak transcription	Pancreas	Pancrea
40	chr1:120310200-120311400	Weak transcription	Small Intestine	intestine
41	chr1:120310200-120311600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr1:120310200-120311600	Active TSS	Fetal Stomach	stomach
43	chr1:120310200-120316200	Weak transcription	Psoas Muscle	Psoas

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