Variant report

Variant	rs3617
Chromosome Location	chr3:52833805-52833806
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52827101..52830669-chr3:52833208..52834941,3	K562	blood:
2	chr3:52803280..52805303-chr3:52832255..52833885,2	MCF-7	breast:
3	chr3:52817973..52820437-chr3:52833631..52835650,3	K562	blood:
4	chr3:52831758..52833558-chr3:52833637..52835171,2	K562	blood:

Variant related genes	Relation type
ENSG00000055957	Chromatin interaction
ENSG00000114904	Chromatin interaction
ENSG00000162267	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1014969	0.82[CHB][hapmap]
rs1029871	0.82[CHB][hapmap]
rs1042779	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10510760	0.82[CHB][hapmap]
rs1075653	0.82[JPT][hapmap]
rs1076425	0.82[JPT][hapmap]
rs10780035	0.82[CHB][hapmap]
rs10865973	0.82[CHB][hapmap]
rs10865974	0.82[CHB][hapmap]
rs1108842	0.82[CHB][hapmap]
rs11130310	0.82[CHB][hapmap]
rs11130312	0.82[CHB][hapmap]
rs11130315	0.82[CHB][hapmap]
rs11130317	0.82[CHB][hapmap]
rs11130323	0.82[CHB][hapmap]
rs11177	0.82[CHB][hapmap]
rs11716747	0.82[CHB][hapmap]
rs11717836	0.80[CHB][hapmap]
rs12487591	0.82[CHB][hapmap]
rs12496634	0.82[CHB][hapmap]
rs12497998	0.82[CHB][hapmap]
rs12635140	0.82[CHB][hapmap]
rs13064064	0.82[CHB][hapmap]
rs13068293	0.82[CHB][hapmap]
rs13071584	0.82[CHB][hapmap]
rs13079063	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs13082208	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs13083798	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs13085895	0.82[CHB][hapmap]
rs1561337	0.82[CHB][hapmap]
rs1866268	0.82[CHB][hapmap]
rs2019065	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2028216	0.82[CHB][hapmap]
rs2071044	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071506	0.82[JPT][hapmap]
rs2071507	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2071508	0.82[JPT][hapmap]
rs2072390	0.82[CHB][hapmap]
rs2079929	0.82[CHB][hapmap]
rs2083180	0.82[CHB][hapmap]
rs2159644	0.82[CHB][hapmap]
rs2164885	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2230535	0.82[CHB][hapmap]
rs2239549	0.82[JPT][hapmap]
rs2239551	0.82[JPT][hapmap]
rs2240919	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2240920	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2268023	0.82[JPT][hapmap]
rs2268025	0.82[CHB][hapmap]
rs2268026	0.82[CHB][hapmap]
rs2268027	0.80[CHB][hapmap]
rs2270197	0.82[JPT][hapmap]
rs2276824	0.82[CHB][hapmap]
rs2286798	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2289247	0.82[CHB][hapmap]
rs2289250	0.82[CHB][hapmap]
rs2300149	0.82[JPT][hapmap]
rs2302417	0.82[EUR][1000 genomes]
rs2336149	0.82[CHB][hapmap]
rs2336545	0.82[CHB][hapmap]
rs2535627	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2535629	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2710323	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33967311	0.82[CHB][hapmap]
rs34017441	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs35526119	0.82[CHB][hapmap]
rs3733039	0.82[CHB][hapmap]
rs3733041	0.82[CHB][hapmap]
rs3733045	0.82[CHB][hapmap]
rs3755806	0.82[CHB][hapmap]
rs3774354	0.82[JPT][hapmap]
rs3774365	0.82[CHB][hapmap]
rs3774366	0.82[CHB][hapmap]
rs4481150	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687548	0.82[CHB][hapmap]
rs4687550	0.82[JPT][hapmap]
rs4687638	0.82[CHB][hapmap]
rs6445534	0.82[CHB][hapmap]
rs6445535	0.82[CHB][hapmap]
rs6617	0.82[CHB][hapmap]
rs6762813	0.82[CHB][hapmap]
rs6778329	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs678	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6795646	0.80[MEX][hapmap]
rs6804145	0.82[CHB][hapmap]
rs6976	0.82[CHB][hapmap]
rs736408	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7611731	0.82[CHB][hapmap]
rs7622694	0.82[CHB][hapmap]
rs7624716	0.82[CHB][hapmap]
rs767418	0.82[CHB][hapmap]
rs8906	0.82[CHB][hapmap]
rs9324	0.82[JPT][hapmap]
rs9860296	0.80[MEX][hapmap]
rs9879090	0.81[CHB][hapmap]
rs9881468	0.82[JPT][hapmap]
rs998909	0.81[CHB][hapmap];0.80[JPT][hapmap]

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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3452194	chr3:52832512-52836010	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs3617	GLT8D1	cis	lymphoblastoid	seeQTL
rs3617	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs3617	ITIH4	cis	parietal	SCAN
rs3617	NT5DC2	cis	multi-tissue	Pritchard
rs3617	WDR6	cis	cerebellum	SCAN
rs3617	FLJ12442	cis	multi-tissue	Pritchard
rs3617	NEK4	cis	parietal	SCAN
rs3617	GLYCTK	cis	parietal	SCAN
rs3617	GNL3	cis	cerebellum	SCAN
rs3617	ITIH4	cis	Lymphoblastoid	GTEx
rs3617	ITIH4	cis	multi-tissue	Pritchard
rs3617	SPCS1	cis	parietal	SCAN
rs3617	GNL3	cis	parietal	SCAN
rs3617	SEMA3G	cis	parietal	SCAN
rs3617	ITIH4	cis	lymphoblastoid	seeQTL
rs3617	NEK4	cis	cerebellum	SCAN
rs3617	NT5DC2	cis	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52825800-52836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:52828200-52835800	Weak transcription	HSMMtube	muscle
3	chr3:52829000-52834200	Weak transcription	Brain Substantia Nigra	brain
4	chr3:52830400-52834000	Genic enhancers	HepG2	liver
5	chr3:52830400-52836400	Weak transcription	Pancreas	Pancrea
6	chr3:52830800-52835000	Genic enhancers	Liver	Liver
7	chr3:52833000-52836200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52833000-52836400	Weak transcription	HSMM	muscle
9	chr3:52833200-52834000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:52833200-52834000	Enhancers	Fetal Thymus	thymus
11	chr3:52833200-52835600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:52833600-52834800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:52833600-52835800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:52833800-52834400	Enhancers	Right Ventricle	heart
15	chr3:52833800-52834600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:52833800-52834600	Enhancers	Spleen	Spleen

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