Variant report

Variant	rs9868112
Chromosome Location	chr3:112329334-112329335
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	ATF1	chr3:112328988-112329362	K562	blood:	n/a	n/a
2	CREB1	chr3:112329008-112329340	GM12878	blood:	n/a	chr3:112329151-112329164
3	POLR2A	chr3:112328617-112329409	U87	brain:	n/a	n/a
4	MAX	chr3:112328990-112329337	NB4	blood:	n/a	n/a
5	CREB1	chr3:112328901-112329441	K562	blood:	n/a	chr3:112329151-112329164
6	POLR2A	chr3:112328686-112329454	U87	brain:	n/a	n/a
7	POLR2A	chr3:112328686-112329402	U87	brain:	n/a	n/a

Variant related genes	Relation type
CCDC80	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11711357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732817	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs4682110	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs72622328	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288953	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9831088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9855848	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers 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	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9868112	GAP43	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
3	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:112300200-112331000	Weak transcription	Lung	lung
6	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
7	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
9	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
11	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:112312600-112330400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
15	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:112316400-112333600	Weak transcription	A549	lung
17	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:112318000-112341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:112318200-112330600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:112322200-112337200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:112322800-112329400	Strong transcription	Colon Smooth Muscle	Colon
22	chr3:112323400-112332400	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr3:112323800-112334600	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:112324400-112331200	Strong transcription	Adipose Nuclei	Adipose
25	chr3:112324600-112331800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:112324800-112330600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:112325000-112329400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:112325200-112329800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:112325400-112329400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:112325600-112330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:112326000-112333400	Weak transcription	Ovary	ovary
32	chr3:112326200-112330000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:112327200-112330600	Weak transcription	Fetal Heart	heart
34	chr3:112327200-112331200	Weak transcription	HUVEC	blood vessel
35	chr3:112327200-112331600	Weak transcription	Fetal Lung	lung
36	chr3:112327600-112330400	Weak transcription	NHLF	lung
37	chr3:112327800-112330200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:112327800-112340600	Weak transcription	Fetal Kidney	kidney
39	chr3:112328200-112332200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:112328400-112332600	Genic enhancers	Osteobl	bone
41	chr3:112328600-112329600	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr3:112328600-112329600	Genic enhancers	HSMM	muscle
43	chr3:112328600-112329600	Enhancers	K562	blood
44	chr3:112328600-112329600	Genic enhancers	NHDF-Ad	bronchial
45	chr3:112328600-112332600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:112328800-112329400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:112328800-112329600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
48	chr3:112329000-112329400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:112329000-112329400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:112329000-112331600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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