Variant report

Variant	rs2989946
Chromosome Location	chr1:227178948-227178949
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	JUND	chr1:227178853-227178959	K562	blood:	n/a	n/a
2	EP300	chr1:227178862-227178995	K562	blood:	n/a	n/a
3	POLR2A	chr1:227169948-227179599	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227127714..227130249-chr1:227177075..227179669,4	K562	blood:
2	chr1:227176748..227179639-chr1:227203696..227206126,2	K562	blood:
3	chr1:227127479..227129517-chr1:227178740..227180378,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233706	TF binding region
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2777834	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2802275	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2989946	SNAP47	cis	parietal	SCAN
rs2989946	ITPKB	cis	parietal	SCAN
rs2989946	ACBD3	cis	cerebellum	SCAN
rs2989946	CDC42BPA	cis	Muscle Skeletal	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
3	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:227162400-227181600	Weak transcription	NHEK	skin
6	chr1:227163000-227180000	Weak transcription	HSMM	muscle
7	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:227163800-227180400	Weak transcription	Fetal Brain Male	brain
9	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:227174800-227179400	Enhancers	Stomach Mucosa	stomach
11	chr1:227174800-227182000	Weak transcription	NHDF-Ad	bronchial
12	chr1:227175200-227181200	Strong transcription	Fetal Muscle Leg	muscle
13	chr1:227175200-227198400	Weak transcription	A549	lung
14	chr1:227175200-227210200	Weak transcription	HMEC	breast
15	chr1:227175400-227182600	Genic enhancers	Fetal Intestine Small	intestine
16	chr1:227175600-227179000	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr1:227175600-227179200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:227175600-227180600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:227175600-227181600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:227175600-227182200	Weak transcription	Brain Germinal Matrix	brain
21	chr1:227175600-227183200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:227175800-227179000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:227175800-227180400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:227175800-227181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:227175800-227181800	Enhancers	Fetal Intestine Large	intestine
27	chr1:227176000-227179200	Enhancers	HepG2	liver
28	chr1:227176000-227181800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:227176000-227181800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:227176000-227190200	Weak transcription	Esophagus	oesophagus
31	chr1:227176000-227191800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:227176000-227216400	Weak transcription	NHLF	lung
33	chr1:227176200-227181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:227176400-227179400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:227176400-227180200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:227176400-227180200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:227176400-227190400	Weak transcription	Osteobl	bone
38	chr1:227176600-227179400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:227176600-227181800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:227176600-227182400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:227176600-227190000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:227176800-227180000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:227176800-227180400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:227176800-227181400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:227177000-227181600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:227177000-227181600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:227177000-227181800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:227177000-227181800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:227177200-227179400	Enhancers	HUVEC	blood vessel
50	chr1:227177200-227180200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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