Variant report

Variant	rs2283938
Chromosome Location	chr22:34140021-34140022
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	SPI1	chr22:34139802-34140061	GM12878	blood:	n/a	n/a
2	BCL3	chr22:34139772-34140140	GM12878	blood:	n/a	n/a
3	SPI1	chr22:34139772-34140073	GM12891	blood:	n/a	n/a
4	REST	chr22:34139847-34140084	Hela-S3	cervix:	n/a	n/a
5	SPI1	chr22:34139676-34140090	GM12891	blood:	n/a	n/a
6	POLR2A	chr22:34139447-34140357	K562	blood:	n/a	n/a
7	SPI1	chr22:34139492-34140233	GM12878	blood:	n/a	n/a
8	SPI1	chr22:34139872-34140054	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIMP3-6	chr22:34139996-34140315	ENSG00000224973.1

Variant related genes	Relation type
LARGE-AS1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1001213	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12157940	0.93[JPT][hapmap]
rs16992904	0.82[CHD][hapmap];0.83[JPT][hapmap]
rs16992908	0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs16992910	0.86[CHB][hapmap]
rs16992923	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs16992929	0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs16992967	0.96[CHD][hapmap];0.87[JPT][hapmap]
rs2267276	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs2267277	0.85[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];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267278	0.93[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267279	0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2267280	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2267281	0.93[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2283934	0.93[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs2283935	0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2283936	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2283937	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs5994791	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs5999080	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5999081	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5999082	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5999084	0.96[CHD][hapmap];0.87[JPT][hapmap]
rs5999086	0.85[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5999087	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62225405	0.82[ASN][1000 genomes]
rs62225407	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1055203	chr22:34098417-34196685	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv459878	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv588936	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1060684	chr22:34108462-34140653	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv524432	chr22:34119866-34146368	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv914992	chr22:34135007-34283144	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2283938	TIMP3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34111200-34146200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr22:34111800-34142800	Weak transcription	Fetal Intestine Small	intestine
3	chr22:34123200-34152000	Weak transcription	Aorta	Aorta
4	chr22:34123800-34140800	Weak transcription	Fetal Stomach	stomach
5	chr22:34124800-34171000	Weak transcription	Ovary	ovary
6	chr22:34126200-34176200	Weak transcription	Spleen	Spleen
7	chr22:34128600-34143200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr22:34131000-34154200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr22:34133600-34140400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr22:34133800-34147600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:34134000-34140400	Weak transcription	Lung	lung
12	chr22:34134400-34164800	Weak transcription	Brain Anterior Caudate	brain
13	chr22:34135600-34141000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:34136000-34140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr22:34136200-34140600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:34136200-34148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:34136200-34152800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr22:34136200-34152800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr22:34136400-34152600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr22:34136800-34141400	Weak transcription	Right Atrium	heart
21	chr22:34136800-34152600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:34137200-34140200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr22:34137200-34144400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr22:34137200-34151000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr22:34137400-34152600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr22:34137600-34151000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr22:34137800-34152800	Weak transcription	Colon Smooth Muscle	Colon
28	chr22:34138000-34140800	Weak transcription	Fetal Heart	heart
29	chr22:34138000-34144400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr22:34138000-34148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr22:34138000-34152600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr22:34138000-34152800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr22:34138000-34160800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr22:34138600-34140400	Weak transcription	Gastric	stomach
35	chr22:34138600-34141400	Weak transcription	Fetal Muscle Leg	muscle
36	chr22:34138600-34141400	Weak transcription	Psoas Muscle	Psoas
37	chr22:34139200-34140400	Weak transcription	Left Ventricle	heart
38	chr22:34139200-34141200	Enhancers	Primary B cells from peripheral blood	blood
39	chr22:34139400-34140600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr22:34139400-34141000	Enhancers	GM12878-XiMat	blood
41	chr22:34139400-34141600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr22:34139600-34140200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr22:34139800-34142600	Weak transcription	HepG2	liver
44	chr22:34140000-34140400	Weak transcription	Right Ventricle	heart
45	chr22:34140000-34140600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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