Variant report

Variant	rs3649
Chromosome Location	chr15:45909304-45909305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45908544..45910284-chr15:45911212..45913714,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs16945097	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs16946621	1.00[CHB][hapmap]
rs17627219	0.81[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2083728	0.81[CEU][hapmap]
rs35325894	1.00[ASN][1000 genomes]
rs55755923	1.00[ASN][1000 genomes]
rs55806911	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56081351	1.00[ASN][1000 genomes]
rs56190351	1.00[ASN][1000 genomes]
rs56259807	1.00[ASN][1000 genomes]
rs56304405	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56375332	1.00[ASN][1000 genomes]
rs56395216	1.00[ASN][1000 genomes]
rs59593563	0.84[AMR][1000 genomes]
rs60351453	0.86[AMR][1000 genomes]
rs60378269	0.85[AMR][1000 genomes]
rs61209164	0.84[AMR][1000 genomes]
rs68120365	1.00[ASN][1000 genomes]
rs685812	0.80[CEU][hapmap]
rs7164956	0.86[AMR][1000 genomes]
rs7165827	0.86[AMR][1000 genomes]
rs7179265	0.81[CEU][hapmap]
rs7181436	0.81[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72709089	1.00[ASN][1000 genomes]
rs72709092	1.00[ASN][1000 genomes]
rs72713106	0.82[AMR][1000 genomes]
rs72713168	0.84[AMR][1000 genomes]
rs72713169	0.84[AMR][1000 genomes]
rs72713171	0.84[AMR][1000 genomes]
rs72713172	0.84[AMR][1000 genomes]
rs72713177	0.86[AMR][1000 genomes]
rs72713178	0.84[AMR][1000 genomes]
rs72713180	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713182	0.86[AMR][1000 genomes]
rs72713185	0.86[AMR][1000 genomes]
rs72713191	0.84[AMR][1000 genomes]
rs72715008	1.00[ASN][1000 genomes]
rs72715010	1.00[ASN][1000 genomes]
rs72715014	1.00[ASN][1000 genomes]
rs72715019	1.00[ASN][1000 genomes]
rs72715020	1.00[ASN][1000 genomes]
rs72715077	1.00[ASN][1000 genomes]
rs8041902	0.81[CEU][hapmap];0.82[MEX][hapmap];0.81[TSI][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	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a
4	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv3338975	chr15:45909185-45912033	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	esv3431461	chr15:45909285-45911908	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3649	TMEM62	cis	cerebellum	SCAN
rs3649	MGA	cis	parietal	SCAN
rs3649	GPR176	cis	cerebellum	SCAN
rs3649	RPAP1	cis	cerebellum	SCAN
rs3649	SLC30A4	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45896800-45912400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:45898400-45911000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:45898800-45911600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr15:45899600-45912400	Weak transcription	HSMMtube	muscle
5	chr15:45900800-45911800	Weak transcription	Primary B cells from cord blood	blood
6	chr15:45901600-45909400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:45902200-45910200	Weak transcription	Fetal Brain Female	brain
8	chr15:45906200-45909800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:45908400-45909800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:45908600-45909400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr15:45908600-45909600	Enhancers	Hela-S3	cervix
12	chr15:45908600-45909800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:45908600-45909800	Enhancers	NHEK	skin
14	chr15:45908800-45909400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:45908800-45909600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr15:45908800-45909800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:45908800-45909800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr15:45908800-45909800	Enhancers	HMEC	breast
19	chr15:45909000-45909400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:45909000-45909600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:45909000-45909600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:45909000-45909600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr15:45909000-45909600	Enhancers	Duodenum Mucosa	Duodenum
24	chr15:45909200-45909400	Enhancers	HUVEC	blood vessel
25	chr15:45909200-45909600	Enhancers	Sigmoid Colon	Sigmoid Colon

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