Variant report

Variant	rs17049650
Chromosome Location	chr4:119097018-119097019
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10001247	0.95[EUR][1000 genomes]
rs10001520	0.95[EUR][1000 genomes]
rs10004607	0.95[EUR][1000 genomes]
rs10007918	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10012051	0.90[EUR][1000 genomes]
rs10014402	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10019969	0.95[EUR][1000 genomes]
rs10020944	0.95[EUR][1000 genomes]
rs10021970	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10023656	0.95[EUR][1000 genomes]
rs10024765	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10028343	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10028980	0.95[EUR][1000 genomes]
rs10518291	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11930405	0.95[EUR][1000 genomes]
rs11931778	0.95[EUR][1000 genomes]
rs11931869	0.87[EUR][1000 genomes]
rs11934128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11934324	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11935016	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11942654	0.85[EUR][1000 genomes]
rs11944236	1.00[EUR][1000 genomes]
rs11945958	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11946833	1.00[EUR][1000 genomes]
rs11946941	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11947911	0.95[EUR][1000 genomes]
rs13434652	0.95[EUR][1000 genomes]
rs13434825	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1589719	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049622	0.95[EUR][1000 genomes]
rs17049625	0.95[EUR][1000 genomes]
rs17049676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049690	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049693	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049694	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049695	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049697	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049698	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049699	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049700	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17049718	0.87[EUR][1000 genomes]
rs1829910	1.00[EUR][1000 genomes]
rs1829911	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28374287	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28507199	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28515963	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28536042	0.95[EUR][1000 genomes]
rs28562324	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28589481	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648504	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28665669	0.90[EUR][1000 genomes]
rs28667401	0.95[EUR][1000 genomes]
rs28668316	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28683619	0.86[EUR][1000 genomes]
rs28690846	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28734874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28826087	0.85[EUR][1000 genomes]
rs28848859	0.95[EUR][1000 genomes]
rs28851582	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28856120	0.95[EUR][1000 genomes]
rs28882407	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41278063	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41278065	1.00[EUR][1000 genomes]
rs4147036	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4147037	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs4147038	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4147039	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4147040	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41520948	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4557347	0.95[EUR][1000 genomes]
rs60958074	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61390934	0.95[EUR][1000 genomes]
rs6824418	1.00[EUR][1000 genomes]
rs6842491	0.95[EUR][1000 genomes]
rs6845921	0.87[EUR][1000 genomes]
rs6848301	0.95[EUR][1000 genomes]
rs6856765	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919205	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919247	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919251	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919254	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919259	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919272	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72919279	0.95[EUR][1000 genomes]
rs7654652	0.95[EUR][1000 genomes]
rs9968544	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9992747	0.95[EUR][1000 genomes]
rs9998199	0.95[EUR][1000 genomes]
rs9998981	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999336	0.95[EUR][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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1009076	chr4:118949490-119269424	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1001236	chr4:118949490-119271243	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1008236	chr4:118989467-119154024	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999152	chr4:119001143-119138322	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv34038	chr4:119035124-119455391	Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1001138	chr4:119095147-119461837	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv537230	chr4:119095147-119461837	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17049650	SLC1A2	trans	brain	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119094000-119097400	Enhancers	NHLF	lung
2	chr4:119094000-119098400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:119094400-119097200	Enhancers	HMEC	breast
4	chr4:119094400-119097600	Enhancers	Primary hematopoietic stem cells	blood
5	chr4:119094400-119097800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr4:119094600-119097600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:119094600-119101800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:119095200-119097200	Enhancers	Fetal Thymus	thymus
9	chr4:119095400-119097200	Enhancers	Osteobl	bone
10	chr4:119095600-119097200	Enhancers	Primary T cells from cord blood	blood
11	chr4:119095600-119097200	Flanking Active TSS	Dnd41	blood
12	chr4:119096000-119097200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr4:119096200-119097800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:119096200-119102000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr4:119096400-119098000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:119096400-119098400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:119096400-119101800	Weak transcription	NHDF-Ad	bronchial
18	chr4:119096800-119097200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:119096800-119097200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:119096800-119097200	Enhancers	Fetal Intestine Small	intestine
21	chr4:119096800-119102000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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