Variant report

Variant	rs2346747
Chromosome Location	chr3:137854475-137854476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr3:137854397-137854641	SK-N-SH	brain:	n/a	n/a
2	REST	chr3:137854258-137854804	HL-60	blood:	n/a	n/a
3	REST	chr3:137854388-137854667	PFSK-1	brain:	n/a	n/a
4	REST	chr3:137854436-137854652	Hela-S3	cervix:	n/a	n/a
5	SPI1	chr3:137853970-137854630	HL-60	blood:	n/a	chr3:137854210-137854223 chr3:137854211-137854224 chr3:137854178-137854191 chr3:137854382-137854391 chr3:137854381-137854394 chr3:137854179-137854192 chr3:137854213-137854222
6	REST	chr3:137854355-137854628	Hela-S3	cervix:	n/a	n/a
7	REST	chr3:137854334-137854790	ECC-1	luminal epithelium:	n/a	n/a
8	REST	chr3:137854330-137854634	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:137846713..137849373-chr3:137854180..137855933,2	K562	blood:

Variant related genes	Relation type
A4GNT	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1564496	0.82[EUR][1000 genomes]
rs1600697	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2170309	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2219936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246945	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2251550	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2346744	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346745	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622695	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs2622696	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622697	0.82[EUR][1000 genomes]
rs2622699	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622700	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs2622733	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs2622734	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs2622735	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs2622736	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622737	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622739	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622740	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622742	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622743	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622744	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724690	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724691	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724710	0.82[ASN][1000 genomes]
rs2724711	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724712	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs2724725	0.81[EUR][1000 genomes]
rs2724726	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs2724727	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs3732839	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs608594	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs7430414	0.81[ASN][1000 genomes]
rs7613558	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632402	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774803	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs774807	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs774808	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs774810	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs774813	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs774814	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs811811	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs9827617	0.83[ASN][1000 genomes]
rs9840008	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851548	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv2762347	chr3:137851198-137910007	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv998106	chr3:137851198-137934610	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2346747	DBR1	cis	normal skin	skin_eQTL
rs2346747	A4GNT	cis	Artery Tibial	GTEx
rs2346747	A4GNT	cis	Thyroid	GTEx
rs2346747	A4GNT	cis	Nerve Tibial	GTEx
rs2346747	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2346747	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137850600-137856800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:137852200-137859400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:137852600-137856600	Weak transcription	Gastric	stomach
4	chr3:137853200-137856200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr3:137853400-137855000	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:137853400-137855200	Enhancers	Brain Hippocampus Middle	brain
7	chr3:137853400-137857000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:137853400-137857600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:137853400-137857800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:137853600-137855200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:137853600-137857000	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:137853600-137857400	Enhancers	Primary B cells from cord blood	blood
13	chr3:137853800-137854800	Weak transcription	Fetal Intestine Small	intestine
14	chr3:137853800-137855200	Weak transcription	Stomach Mucosa	stomach
15	chr3:137853800-137855600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:137854000-137856600	Weak transcription	Pancreas	Pancrea
17	chr3:137854200-137855000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:137854200-137855000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:137854400-137855200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:137854400-137855400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:137854400-137855400	Enhancers	Brain Substantia Nigra	brain

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