Variant report

Variant	rs13204102
Chromosome Location	chr6:109938944-109938945
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109932824..109934658-chr6:109936171..109939061,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10457192	0.82[ASN][1000 genomes]
rs10499053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10782162	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10782163	0.83[ASN][1000 genomes]
rs10872034	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11153183	0.82[ASN][1000 genomes]
rs11153188	0.88[ASN][1000 genomes]
rs11153214	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11752791	0.90[ASN][1000 genomes]
rs11754340	0.90[ASN][1000 genomes]
rs11754455	0.82[ASN][1000 genomes]
rs11755641	0.91[ASN][1000 genomes]
rs12191353	0.86[ASN][1000 genomes]
rs12192776	0.90[ASN][1000 genomes]
rs12193719	0.91[ASN][1000 genomes]
rs12194061	0.88[ASN][1000 genomes]
rs12194157	0.90[ASN][1000 genomes]
rs12197180	0.81[ASN][1000 genomes]
rs12197838	0.83[ASN][1000 genomes]
rs12197950	0.90[ASN][1000 genomes]
rs12198938	0.82[ASN][1000 genomes]
rs12199154	0.82[ASN][1000 genomes]
rs12205140	0.81[ASN][1000 genomes]
rs12205485	0.92[ASN][1000 genomes]
rs12208018	0.92[ASN][1000 genomes]
rs12208933	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210706	0.83[ASN][1000 genomes]
rs12212476	0.82[ASN][1000 genomes]
rs12214639	0.91[ASN][1000 genomes]
rs12528781	0.92[ASN][1000 genomes]
rs13191066	0.90[ASN][1000 genomes]
rs13199109	0.81[ASN][1000 genomes]
rs13199135	0.91[ASN][1000 genomes]
rs13201947	0.83[ASN][1000 genomes]
rs13201951	0.85[ASN][1000 genomes]
rs13203587	0.82[ASN][1000 genomes]
rs13204500	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321328	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13220915	0.82[ASN][1000 genomes]
rs1406899	0.82[ASN][1000 genomes]
rs1476388	0.83[ASN][1000 genomes]
rs1960325	0.91[ASN][1000 genomes]
rs1980591	0.92[ASN][1000 genomes]
rs1998811	0.82[ASN][1000 genomes]
rs2024849	0.82[ASN][1000 genomes]
rs2024850	0.82[ASN][1000 genomes]
rs2024852	0.82[ASN][1000 genomes]
rs2024853	0.82[ASN][1000 genomes]
rs2148089	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2208209	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277114	0.82[ASN][1000 genomes]
rs2357124	0.84[ASN][1000 genomes]
rs36131450	0.84[ASN][1000 genomes]
rs3899233	0.84[ASN][1000 genomes]
rs4490694	0.91[ASN][1000 genomes]
rs4945833	0.91[ASN][1000 genomes]
rs6568592	0.83[ASN][1000 genomes]
rs68042406	0.86[ASN][1000 genomes]
rs6906216	0.80[ASN][1000 genomes]
rs6911700	0.82[ASN][1000 genomes]
rs6914498	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916579	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6926096	0.80[ASN][1000 genomes]
rs71541003	0.84[ASN][1000 genomes]
rs729888	0.90[ASN][1000 genomes]
rs7341297	0.82[ASN][1000 genomes]
rs749517	0.83[ASN][1000 genomes]
rs7755941	0.82[ASN][1000 genomes]
rs7767525	0.87[ASN][1000 genomes]
rs7773950	0.82[ASN][1000 genomes]
rs971434	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1019389	chr6:109868058-109987502	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv538416	chr6:109868058-109987502	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv917318	chr6:109885195-109982375	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13204102	SMPD2	cis	Whole Blood	GTEx
rs13204102	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs13204102	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs13204102	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs13204102	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs13204102	MICAL1	cis	brain	BrainEAC

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109923600-109952600	Weak transcription	Right Ventricle	heart
2	chr6:109928000-109966400	Weak transcription	Pancreas	Pancrea
3	chr6:109933000-109939400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:109933000-109948800	Weak transcription	Thymus	Thymus
5	chr6:109933000-109962800	Weak transcription	Left Ventricle	heart
6	chr6:109933000-109966400	Weak transcription	Brain Germinal Matrix	brain
7	chr6:109933000-109985200	Weak transcription	Psoas Muscle	Psoas
8	chr6:109933800-109951400	Weak transcription	Primary B cells from cord blood	blood

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