Variant report

Variant	rs2609255
Chromosome Location	chr4:89811195-89811196
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10008568	0.86[CHD][hapmap]
rs10461165	0.82[CHB][hapmap];0.88[CHD][hapmap];0.80[ASN][1000 genomes]
rs1246629	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246631	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246632	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246634	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1246642	1.00[CEU][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12640274	0.81[ASN][1000 genomes]
rs1379932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1379933	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1458551	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563689	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045517	0.84[CHD][hapmap]
rs2085600	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2125409	0.81[ASN][1000 genomes]
rs2446300	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2446301	0.90[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2446303	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446304	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464522	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2464523	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2464528	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609258	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2609259	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2609260	0.84[CHD][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes]
rs2609261	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2609262	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2609264	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609265	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609279	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2609280	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2704570	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2704581	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704582	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704583	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704587	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2704589	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2704604	0.93[CEU][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2869952	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869966	0.84[CHD][hapmap]
rs2869967	0.84[CHD][hapmap]
rs28767574	0.80[ASN][1000 genomes]
rs2904255	0.91[ASN][1000 genomes]
rs4505789	0.81[ASN][1000 genomes]
rs4693974	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs6813090	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6815970	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7671167	0.81[CHD][hapmap]
rs7673818	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9997652	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[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	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	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Interstitial lung disease	23583980	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2609255	HERC3	cis	parietal	SCAN
rs2609255	FAM13A	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89802200-89820600	Weak transcription	Aorta	Aorta
2	chr4:89802600-89812800	Weak transcription	K562	blood
3	chr4:89802600-89825600	Weak transcription	Ovary	ovary
4	chr4:89805400-89817600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:89809200-89828800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:89809400-89813400	Enhancers	Fetal Intestine Small	intestine
7	chr4:89810000-89811400	Enhancers	Placenta	Placenta
8	chr4:89810200-89811400	Enhancers	Psoas Muscle	Psoas
9	chr4:89810200-89811400	Enhancers	HepG2	liver
10	chr4:89810400-89811600	Enhancers	Fetal Intestine Large	intestine
11	chr4:89810800-89811400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:89810800-89811600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr4:89811000-89811400	Enhancers	Gastric	stomach
14	chr4:89811000-89813200	Weak transcription	Primary hematopoietic stem cells	blood

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