Variant report

Variant	rs7548599
Chromosome Location	chr1:185336295-185336296
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185323027..185325964-chr1:185336251..185338084,2	K562	blood:
2	chr1:185334258..185337021-chr1:185337463..185339197,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10157232	0.98[ASN][1000 genomes]
rs10157996	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs10158623	0.98[ASN][1000 genomes]
rs10737258	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10752948	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10911706	0.83[EUR][1000 genomes]
rs10911711	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12044943	0.86[ASN][1000 genomes]
rs2207517	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2207518	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207519	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2224027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2295212	0.83[EUR][1000 genomes]
rs4651253	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6424975	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6424976	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs6656019	0.86[ASN][1000 genomes]
rs6659669	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6665186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679327	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6682074	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66845254	0.98[ASN][1000 genomes]
rs6687774	0.85[CHD][hapmap]
rs6689206	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7512337	0.98[ASN][1000 genomes]
rs7519628	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7531487	0.86[ASN][1000 genomes]
rs7545878	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9988622	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	esv2756872	chr1:185293197-185345771	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2758981	chr1:185293197-185345771	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1008247	chr1:185321360-185345771	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7548599	TOR1AIP1	cis	parietal	SCAN
rs7548599	ARPC5	cis	cerebellum	SCAN
rs7548599	FAM129A	cis	lymphoblastoid	seeQTL
rs7548599	LHX4	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185325400-185336400	Weak transcription	Right Atrium	heart
2	chr1:185334800-185336600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:185334800-185342400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:185335000-185337600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:185335000-185345000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:185335200-185336600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:185335200-185336600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:185335200-185336600	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr1:185335200-185336600	Enhancers	HMEC	breast
10	chr1:185335200-185336800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:185335200-185336800	Enhancers	NHEK	skin
12	chr1:185335200-185337000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:185335400-185336400	Weak transcription	Esophagus	oesophagus
14	chr1:185335400-185336600	Enhancers	Hela-S3	cervix
15	chr1:185335600-185336400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:185335600-185336400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:185335600-185336400	Enhancers	A549	lung
18	chr1:185335600-185336600	Enhancers	Osteobl	bone
19	chr1:185335600-185338600	Enhancers	HUVEC	blood vessel
20	chr1:185335800-185337400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:185336000-185336400	Weak transcription	Stomach Mucosa	stomach
22	chr1:185336200-185338800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:185336200-185339800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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