Variant report

Variant	rs2670625
Chromosome Location	chr4:89978867-89978868
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	RFX5	chr4:89978783-89978981	K562	blood:	n/a	n/a
2	KAP1	chr4:89978404-89979039	K562	blood:	n/a	n/a
3	IRF1	chr4:89976948-89978926	K562	blood:	n/a	chr4:89977624-89977637 chr4:89977623-89977637 chr4:89978870-89978880 chr4:89977626-89977636 chr4:89978508-89978521 chr4:89977626-89977640 chr4:89977622-89977636 chr4:89977624-89977637 chr4:89977624-89977638

No.	Distal block	Cell Line	Cell type
1	chr4:89743956..89746323-chr4:89976893..89978969,2	K562	blood:
2	chr4:89920516..89923501-chr4:89978516..89980046,2	K562	blood:
3	chr4:89977166..89979264-chr4:90032025..90033904,2	K562	blood:
4	chr4:89978596..89980145-chr4:89983083..89985851,2	K562	blood:

Variant related genes	Relation type
FAM13A	TF binding region
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10009665	0.89[ASN][1000 genomes]
rs11097214	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12509747	0.88[ASN][1000 genomes]
rs12641645	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12643834	0.88[ASN][1000 genomes]
rs12644568	0.88[ASN][1000 genomes]
rs12646713	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12646734	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124770	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13148714	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1355835	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355838	0.89[ASN][1000 genomes]
rs1513821	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1533291	0.89[JPT][hapmap]
rs17015025	0.82[CHD][hapmap];0.93[GIH][hapmap]
rs1708661	0.89[JPT][hapmap]
rs1708674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1708678	0.89[JPT][hapmap]
rs1708684	0.89[JPT][hapmap]
rs17770293	0.93[GIH][hapmap]
rs1795721	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1795731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795733	0.89[JPT][hapmap]
rs2037036	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2037037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2280099	0.82[CHD][hapmap];0.93[GIH][hapmap]
rs2458545	0.89[JPT][hapmap]
rs2458546	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2458547	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2464516	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2464517	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2670624	0.89[JPT][hapmap]
rs2670626	0.89[JPT][hapmap]
rs2670629	0.89[JPT][hapmap]
rs2670630	0.89[JPT][hapmap]
rs2704597	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2869988	0.88[ASN][1000 genomes]
rs2869990	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634189	0.88[ASN][1000 genomes]
rs4693221	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4693983	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6532094	0.89[JPT][hapmap]
rs6532099	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532109	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6532112	0.88[ASN][1000 genomes]
rs6822256	0.93[GIH][hapmap]
rs6833401	0.93[ASN][1000 genomes]
rs6833424	0.91[ASN][1000 genomes]
rs6833576	0.93[ASN][1000 genomes]
rs6835031	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6844490	0.89[JPT][hapmap]
rs6854285	0.88[ASN][1000 genomes]
rs72665891	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7440590	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs756175	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs756176	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7691983	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7696844	0.88[ASN][1000 genomes]
rs938264	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9991151	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv461577	chr4:89904124-89986326	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv594807	chr4:89904124-89986326	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2670625	FAM190A	cis	parietal	SCAN
rs2670625	FAM13A	cis	cerebellum	SCAN
rs2670625	KLHL8	cis	parietal	SCAN
rs2670625	CHST3	trans	parietal	SCAN
rs2670625	MAPK10	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89975200-89979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:89976600-89979000	Active TSS	Stomach Smooth Muscle	stomach
3	chr4:89976600-89979000	Active TSS	K562	blood
4	chr4:89977400-89979000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:89978000-89979000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr4:89978600-89979000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:89978800-89979000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:89978800-89979000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:89978800-89979000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:89978800-89979000	Enhancers	Fetal Lung	lung
11	chr4:89978800-89979000	Enhancers	Fetal Stomach	stomach
12	chr4:89978800-89979000	Enhancers	Rectal Smooth Muscle	rectum
13	chr4:89978800-89979000	Enhancers	Osteobl	bone
14	chr4:89978800-89979200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:89978800-89979200	Enhancers	Primary hematopoietic stem cells	blood
16	chr4:89978800-89979200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:89978800-89979200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:89978800-89979200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:89978800-89979200	Enhancers	Esophagus	oesophagus
20	chr4:89978800-89979200	Enhancers	Fetal Kidney	kidney
21	chr4:89978800-89979200	Enhancers	Pancreas	Pancrea

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