Variant report

Variant	rs10499052
Chromosome Location	chr6:109885475-109885476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10499053	0.80[CEU][hapmap]
rs10782162	0.80[CEU][hapmap]
rs11753645	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs11964533	0.89[CEU][hapmap]
rs11968891	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12208933	0.80[CEU][hapmap]
rs12529505	1.00[CEU][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12661287	0.94[CEU][hapmap];0.85[CHB][hapmap]
rs13191995	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13195462	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13195517	0.89[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs13199088	0.88[AMR][1000 genomes]
rs13199519	0.94[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs13203636	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs13204787	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13211604	0.94[CEU][hapmap];0.92[CHB][hapmap]
rs1321328	0.80[CEU][hapmap]
rs13214717	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13215994	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1322818	1.00[CEU][hapmap]
rs28823411	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34533653	0.89[AFR][1000 genomes]
rs3799835	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs4428538	0.89[AFR][1000 genomes]
rs971434	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv7953	chr6:109885153-109893563	Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10499052	SMPD2	cis	Whole Blood	GTEx
rs10499052	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs10499052	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs10499052	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109867000-109885800	Weak transcription	Ovary	ovary
2	chr6:109878400-109886200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:109878800-109894000	Weak transcription	Pancreas	Pancrea
4	chr6:109878800-109903600	Weak transcription	Psoas Muscle	Psoas
5	chr6:109879000-109903800	Weak transcription	Thymus	Thymus
6	chr6:109879000-109906000	Weak transcription	Left Ventricle	heart
7	chr6:109879000-109917400	Weak transcription	Aorta	Aorta
8	chr6:109879400-109893400	Weak transcription	Primary T cells from cord blood	blood
9	chr6:109879600-109886400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:109879800-109900600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:109880800-109900000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:109881000-109900000	Weak transcription	Adipose Nuclei	Adipose
13	chr6:109881200-109902400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr6:109883400-109886200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:109884000-109885600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:109884000-109886200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:109885000-109886000	Strong transcription	Primary B cells from cord blood	blood
18	chr6:109885000-109886600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:109885000-109902400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:109885200-109900200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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